Mercurial > repos > peterjc > blastxml_to_top_descr

changeset 11:98f8431dab44 draft

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Uploaded v0.1.0, now also handles extended tabular BLAST output.
author peterjc
date Fri, 13 Jun 2014 07:07:35 -0400
parents 09a68a90d552
children fe1ed74793c9
files blastxml_to_top_descr/README.rst blastxml_to_top_descr/blastxml_to_top_descr.py blastxml_to_top_descr/blastxml_to_top_descr.xml blastxml_to_top_descr/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.py tools/blastxml_to_top_descr/blastxml_to_top_descr.xml tools/blastxml_to_top_descr/repository_dependencies.xml
diffstat 12 files changed, 1154 insertions(+), 962 deletions(-) [+]
line wrap: on
line diff
--- a/blastxml_to_top_descr/README.rst	Wed Sep 18 06:07:53 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,121 +0,0 @@
-Galaxy tool to extract top BLAST hit descriptions from BLAST XML
-================================================================
-
-This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script to parse a BLAST XML file, and extract the
-identifiers with description for the top matches (by default the top 3), and
-output these as a simple tabular file along with the query identifiers.
-
-It is available from the Galaxy Tool Shed at:
-http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
-
-This requires the 'blast_datatypes' repository from the Galaxy Tool Shed
-to provide the 'blastxml' file format definition.
-
-
-Automated Installation
-======================
-
-This should be straightforward, Galaxy should automatically install the
-'blast_datatypes' dependency.
-
-
-Manual Installation
-===================
-
-If you haven't done so before, first install the 'blast_datatypes' repository.
-
-There are just two files to install (if doing this manually):
-
-* blastxml_to_top_descr.py (the Python script)
-* blastxml_to_top_descr.xml (the Galaxy tool definition)
-
-The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to
-the NCBI BLAST+ tool wrappers.
-
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer
-the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line::
-
-    <tool file="ncbi_blast_plus/blastxml_to_top_descr.xml" />
-
-To run the tool's tests, also add this line to tools_conf.xml.sample then::
-
-    $ sh run_functional_tests.sh -id blastxml_to_top_descr
-
-
-History
-=======
-
-======= ======================================================================
-Version Changes
-------- ----------------------------------------------------------------------
-v0.0.1  - Initial version.
-v0.0.2  - Since BLAST+ was moved out of the Galaxy core, now have a dependency
-          on the 'blast_datatypes' repository in the Tool Shed.
-v0.0.3  - Include the test files required to run the unit tests
-v0.0.4  - Quote filenames in case they contain spaces (internal change)
-v0.0.5  - Include number of queries with BLAST matches in stdout (peek text)
-v0.0.6  - Check for errors via the script's return code (internal change)
-v0.0.7  - Link to Tool Shed added to help text and this documentation.
-        - Tweak dependency on blast_datatypes to also work on Test Tool Shed
-        - Adopt standard MIT License.
-v0.0.8  - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
-v0.0.9  - Updated citation information (Cock et al. 2013).
-======= ======================================================================
-
-
-Bug Reports
-===========
-
-You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
-us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
-
-
-Developers
-==========
-
-This script and related tools were originally developed on the 'tools' branch of
-the following Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/
-
-As of July 2013, development is continuing on a dedicated GitHub repository:
-https://github.com/peterjc/galaxy_blast
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the GitHub repository root folder::
-
-    $ tar -czf blastxml_to_top_descr.tar.gz blastxml_to_top_descr/README.rst blastxml_to_top_descr/blastxml_to_top_descr.* blastxml_to_top_descr/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular
-
-Check this worked::
-
-    $ tar -tzf blastxml_to_top_descr.tar.gz
-    blastxml_to_top_descr/README.rst
-    blastxml_to_top_descr/blastxml_to_top_descr.py
-    blastxml_to_top_descr/blastxml_to_top_descr.xml
-    blastxml_to_top_descr/repository_dependencies.xml
-    test-data/blastp_four_human_vs_rhodopsin.xml
-    test-data/blastp_four_human_vs_rhodopsin_top3.tabular
-
-
-Licence (MIT)
-=============
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
--- a/blastxml_to_top_descr/blastxml_to_top_descr.py	Wed Sep 18 06:07:53 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-#!/usr/bin/env python
-"""Convert a BLAST XML file to a top hits description table.
-
-Takes three command line options, input BLAST XML filename, output tabular
-BLAST filename, number of hits to collect the descriptions of.
-"""
-import sys
-import re
-
-if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.5"
-    sys.exit(0)
-
-if sys.version_info[:2] >= ( 2, 5 ):
-    import xml.etree.cElementTree as ElementTree
-else:
-    from galaxy import eggs
-    import pkg_resources; pkg_resources.require( "elementtree" )
-    from elementtree import ElementTree
-
-def stop_err( msg ):
-    sys.stderr.write("%s\n" % msg)
-    sys.exit(1)
-
-#Parse Command Line
-try:
-    in_file, out_file, topN = sys.argv[1:]
-except:
-    stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, number of hits")
-
-
-try:
-    topN = int(topN)
-except ValueError:
-    stop_err("Number of hits  argument should be an integer (at least 1)")
-if topN < 1:
-    stop_err("Number of hits  argument should be an integer (at least 1)")
-
-# get an iterable
-try: 
-    context = ElementTree.iterparse(in_file, events=("start", "end"))
-except:
-    stop_err("Invalid data format.")
-# turn it into an iterator
-context = iter(context)
-# get the root element
-try:
-    event, root = context.next()
-except:
-    stop_err( "Invalid data format." )
-
-
-re_default_query_id = re.compile("^Query_\d+$")
-assert re_default_query_id.match("Query_101")
-assert not re_default_query_id.match("Query_101a")
-assert not re_default_query_id.match("MyQuery_101")
-re_default_subject_id = re.compile("^Subject_\d+$")
-assert re_default_subject_id.match("Subject_1")
-assert not re_default_subject_id.match("Subject_")
-assert not re_default_subject_id.match("Subject_12a")
-assert not re_default_subject_id.match("TheSubject_1")
-
-
-count = 0
-pos_count = 0
-outfile = open(out_file, 'w')
-outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN)))
-for event, elem in context:
-    # for every <Iteration> tag
-    if event == "end" and elem.tag == "Iteration":
-        #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
-        # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-        # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-        # <Iteration_query-len>406</Iteration_query-len>
-        # <Iteration_hits></Iteration_hits>
-        #
-        #Or, from BLAST 2.2.24+ run online
-        # <Iteration_query-ID>Query_1</Iteration_query-ID>
-        # <Iteration_query-def>Sample</Iteration_query-def>
-        # <Iteration_query-len>516</Iteration_query-len>
-        # <Iteration_hits>...
-        qseqid = elem.findtext("Iteration_query-ID")
-        if qseqid is None:
-            stop_err("Missing <Iteration_query-ID> (could be really old BLAST XML data?)")
-        if re_default_query_id.match(qseqid):
-            #Place holder ID, take the first word of the query definition
-            qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
-        # for every <Hit> within <Iteration>
-        hit_descrs = []
-        for hit in elem.findall("Iteration_hits/Hit"):
-            #Expecting either this,
-            # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
-            # <Hit_def>RecName: Full=Rhodopsin</Hit_def>
-            # <Hit_accession>P56514</Hit_accession>
-            #or,
-            # <Hit_id>Subject_1</Hit_id>
-            # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>
-            # <Hit_accession>Subject_1</Hit_accession>
-            #
-            #apparently depending on the parse_deflines switch
-            sseqid = hit.findtext("Hit_id").split(None,1)[0]
-            hit_def = sseqid + " " + hit.findtext("Hit_def")
-            if re_default_subject_id.match(sseqid) \
-            and sseqid == hit.findtext("Hit_accession"):
-                #Place holder ID, take the first word of the subject definition
-                hit_def = hit.findtext("Hit_def")
-                sseqid = hit_def.split(None,1)[0]
-            assert hit_def not in hit_descrs
-            hit_descrs.append(hit_def)
-        #print "%r has %i hits" % (qseqid, len(hit_descrs))
-        if hit_descrs:
-            pos_count += 1
-        hit_descrs = hit_descrs[:topN]
-        while len(hit_descrs) < topN:
-            hit_descrs.append("")
-        outfile.write("%s\t%s\n" % (qseqid, "\t".join(hit_descrs)))
-        count += 1
-        # prevents ElementTree from growing large datastructure
-        root.clear()
-        elem.clear()
-outfile.close()
-print "Of %i queries, %i had BLAST results" % (count, pos_count)
--- a/blastxml_to_top_descr/blastxml_to_top_descr.xml	Wed Sep 18 06:07:53 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.9">
-    <description>Make a table from BLAST XML</description>
-    <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command>
-    <command interpreter="python">
-      blastxml_to_top_descr.py "${blastxml_file}" "${tabular_file}" ${topN}
-    </command>
-    <stdio>
-        <!-- Assume anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <inputs>
-        <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> 
-	<param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/>
-    </inputs>
-    <outputs>
-        <data name="tabular_file" format="tabular" label="Top $topN descriptions from $blastxml_file.name" />
-    </outputs>
-    <requirements>
-    </requirements>
-    <tests>
-        <test>
-            <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
-            <param name="topN" value="3" />
-            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" />
-        </test>
-    </tests>
-    <help>
-
-**What it does**
-
-NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
-formats including text, tabular and a more detailed XML format. You can
-do a lot of things with tabular files in Galaxy (sorting, filtering, joins,
-etc) however currently the BLAST tabular output omits the hit descriptions
-found in the other output formats.
-
-This tool turns a BLAST XML file into a simple tabular file containing
-one row per query sequence, containing the query identifier and then
-the three (by default) top hit descriptions. If a query doesn't have
-that many hits, then these entries are left blank.
-
-**Example Usage**
-
-One simple usage would be to take a transcriptome assembly or set of
-gene predictions, run a BLAST search against the NCBI NR database, and
-then use this tool to make a table of the top three BLAST hits. This
-can give you a 'quick and dirty' crude annotation, potentially enough
-to spot some problems (e.g. bacterial contaimination could be very
-obvious).
-
-**References**
-
-If you use this Galaxy tool in work leading to a scientific publication please
-cite:
-
-Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
-Galaxy tools and workflows for sequence analysis with applications
-in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
-
-This wrapper is available to install into other Galaxy Instances via the Galaxy
-Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
-
-    </help>
-</tool>
--- a/blastxml_to_top_descr/repository_dependencies.xml	Wed Sep 18 06:07:53 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Requires BLAST XML and database datatype definitions.">
-<repository changeset_revision="b3a3ba0c1d47" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-</repositories>
--- a/test-data/blastp_four_human_vs_rhodopsin.xml	Wed Sep 18 06:07:53 2013 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin.xml	Fri Jun 13 07:07:35 2014 -0400
@@ -2,7 +2,7 @@
 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
 <BlastOutput>
   <BlastOutput_program>blastp</BlastOutput_program>
-  <BlastOutput_version>BLASTP 2.2.26+</BlastOutput_version>
+  <BlastOutput_version>BLASTP 2.2.29+</BlastOutput_version>
   <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
   <BlastOutput_db></BlastOutput_db>
   <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID>
@@ -17,630 +17,649 @@
       <Parameters_filter>F</Parameters_filter>
     </Parameters>
   </BlastOutput_param>
-  <BlastOutput_iterations>
-    <Iteration>
-      <Iteration_iter-num>1</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>2</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>3</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>4</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>5</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>6</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>406</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>30</Statistics_hsp-len>
-          <Statistics_eff-space>119568</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>7</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>8</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>9</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>10</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>11</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>12</Iteration_iter-num>
-      <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
-      <Iteration_query-len>1161</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>38</Statistics_hsp-len>
-          <Statistics_eff-space>348130</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>13</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>14</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>15</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>16</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>17</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>18</Iteration_iter-num>
-      <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
-      <Iteration_query-len>1382</Iteration_query-len>
-      <Iteration_hits></Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>39</Statistics_hsp-len>
-          <Statistics_eff-space>414987</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-      <Iteration_message>No hits found</Iteration_message>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>19</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|57163783|ref|NP_001009242.1|</Hit_id>
-          <Hit_def>rhodopsin [Felis catus]</Hit_def>
-          <Hit_accession>NP_001009242</Hit_accession>
-          <Hit_len>348</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>701.049</Hsp_bit-score>
-              <Hsp_score>1808</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>348</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>336</Hsp_identity>
-              <Hsp_positive>343</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>20</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
-          <Hit_def>RecName: Full=Rhodopsin</Hit_def>
-          <Hit_accession>P56514</Hit_accession>
-          <Hit_len>354</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>619.002</Hsp_bit-score>
-              <Hsp_score>1595</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>342</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>290</Hsp_identity>
-              <Hsp_positive>322</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>21</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|283855846|gb|ADB45242.1|</Hit_id>
-          <Hit_def>rhodopsin [Cynopterus brachyotis]</Hit_def>
-          <Hit_accession>ADB45242</Hit_accession>
-          <Hit_len>328</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>653.284</Hsp_bit-score>
-              <Hsp_score>1684</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>338</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>328</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>311</Hsp_identity>
-              <Hsp_positive>321</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>328</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>22</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|283855823|gb|ADB45229.1|</Hit_id>
-          <Hit_def>rhodopsin [Myotis pilosus]</Hit_def>
-          <Hit_accession>ADB45229</Hit_accession>
-          <Hit_len>328</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>631.328</Hsp_bit-score>
-              <Hsp_score>1627</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>11</Hsp_query-from>
-              <Hsp_query-to>338</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>328</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>311</Hsp_identity>
-              <Hsp_positive>323</Hsp_positive>
-              <Hsp_gaps>0</Hsp_gaps>
-              <Hsp_align-len>328</Hsp_align-len>
-              <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq>
-              <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq>
-              <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>23</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|223523|prf||0811197A</Hit_id>
-          <Hit_def>rhodopsin [Bos taurus]</Hit_def>
-          <Hit_accession>0811197A</Hit_accession>
-          <Hit_len>347</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>673.315</Hsp_bit-score>
-              <Hsp_score>1736</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>348</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>347</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>324</Hsp_identity>
-              <Hsp_positive>336</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>348</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-    <Iteration>
-      <Iteration_iter-num>24</Iteration_iter-num>
-      <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
-      <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
-      <Iteration_query-len>348</Iteration_query-len>
-      <Iteration_hits>
-        <Hit>
-          <Hit_num>1</Hit_num>
-          <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id>
-          <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def>
-          <Hit_accession>BAB21486</Hit_accession>
-          <Hit_len>354</Hit_len>
-          <Hit_hsps>
-            <Hsp>
-              <Hsp_num>1</Hsp_num>
-              <Hsp_bit-score>599.356</Hsp_bit-score>
-              <Hsp_score>1544</Hsp_score>
-              <Hsp_evalue>0</Hsp_evalue>
-              <Hsp_query-from>1</Hsp_query-from>
-              <Hsp_query-to>341</Hsp_query-to>
-              <Hsp_hit-from>1</Hsp_hit-from>
-              <Hsp_hit-to>342</Hsp_hit-to>
-              <Hsp_query-frame>0</Hsp_query-frame>
-              <Hsp_hit-frame>0</Hsp_hit-frame>
-              <Hsp_identity>281</Hsp_identity>
-              <Hsp_positive>314</Hsp_positive>
-              <Hsp_gaps>1</Hsp_gaps>
-              <Hsp_align-len>342</Hsp_align-len>
-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>
-              <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>
-              <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV  TW MALACA PPL GWSRYIPEGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP   +D ASAT SKTE</Hsp_midline>
-            </Hsp>
-          </Hit_hsps>
-        </Hit>
-      </Iteration_hits>
-      <Iteration_stat>
-        <Statistics>
-          <Statistics_db-num>0</Statistics_db-num>
-          <Statistics_db-len>0</Statistics_db-len>
-          <Statistics_hsp-len>29</Statistics_hsp-len>
-          <Statistics_eff-space>101761</Statistics_eff-space>
-          <Statistics_kappa>0.041</Statistics_kappa>
-          <Statistics_lambda>0.267</Statistics_lambda>
-          <Statistics_entropy>0.14</Statistics_entropy>
-        </Statistics>
-      </Iteration_stat>
-    </Iteration>
-  </BlastOutput_iterations>
-</BlastOutput>
\ No newline at end of file
+<BlastOutput_iterations>
+<Iteration>
+  <Iteration_iter-num>1</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>406</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>30</Statistics_hsp-len>
+      <Statistics_eff-space>119568</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>2</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>406</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>30</Statistics_hsp-len>
+      <Statistics_eff-space>119568</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>3</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>406</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>30</Statistics_hsp-len>
+      <Statistics_eff-space>119568</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>4</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>406</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>30</Statistics_hsp-len>
+      <Statistics_eff-space>119568</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>5</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>406</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>30</Statistics_hsp-len>
+      <Statistics_eff-space>119568</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>6</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>406</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>30</Statistics_hsp-len>
+      <Statistics_eff-space>119568</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>7</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
+  <Iteration_query-len>1161</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>38</Statistics_hsp-len>
+      <Statistics_eff-space>348130</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>8</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
+  <Iteration_query-len>1161</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>38</Statistics_hsp-len>
+      <Statistics_eff-space>348130</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>9</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
+  <Iteration_query-len>1161</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>38</Statistics_hsp-len>
+      <Statistics_eff-space>348130</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>10</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
+  <Iteration_query-len>1161</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>38</Statistics_hsp-len>
+      <Statistics_eff-space>348130</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>11</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
+  <Iteration_query-len>1161</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>38</Statistics_hsp-len>
+      <Statistics_eff-space>348130</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>12</Iteration_iter-num>
+  <Iteration_query-ID>sp|Q9NSY1|BMP2K_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2</Iteration_query-def>
+  <Iteration_query-len>1161</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>38</Statistics_hsp-len>
+      <Statistics_eff-space>348130</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>13</Iteration_iter-num>
+  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
+  <Iteration_query-len>1382</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>39</Statistics_hsp-len>
+      <Statistics_eff-space>414987</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>14</Iteration_iter-num>
+  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
+  <Iteration_query-len>1382</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>39</Statistics_hsp-len>
+      <Statistics_eff-space>414987</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>15</Iteration_iter-num>
+  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
+  <Iteration_query-len>1382</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>39</Statistics_hsp-len>
+      <Statistics_eff-space>414987</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>16</Iteration_iter-num>
+  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
+  <Iteration_query-len>1382</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>39</Statistics_hsp-len>
+      <Statistics_eff-space>414987</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>17</Iteration_iter-num>
+  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
+  <Iteration_query-len>1382</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>39</Statistics_hsp-len>
+      <Statistics_eff-space>414987</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>18</Iteration_iter-num>
+  <Iteration_query-ID>sp|P06213|INSR_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4</Iteration_query-def>
+  <Iteration_query-len>1382</Iteration_query-len>
+<Iteration_hits>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>39</Statistics_hsp-len>
+      <Statistics_eff-space>414987</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+  <Iteration_message>No hits found</Iteration_message>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>19</Iteration_iter-num>
+  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>348</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gi|57163783|ref|NP_001009242.1|</Hit_id>
+  <Hit_def>rhodopsin [Felis catus]</Hit_def>
+  <Hit_accession>NP_001009242</Hit_accession>
+  <Hit_len>348</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>701.049</Hsp_bit-score>
+      <Hsp_score>1808</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>348</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>348</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>336</Hsp_identity>
+      <Hsp_positive>343</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>348</Hsp_align-len>
+      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
+      <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA</Hsp_hseq>
+      <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>29</Statistics_hsp-len>
+      <Statistics_eff-space>101761</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>20</Iteration_iter-num>
+  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>348</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
+  <Hit_def>RecName: Full=Rhodopsin</Hit_def>
+  <Hit_accession>P56514</Hit_accession>
+  <Hit_len>354</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>619.002</Hsp_bit-score>
+      <Hsp_score>1595</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>341</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>342</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>290</Hsp_identity>
+      <Hsp_positive>322</Hsp_positive>
+      <Hsp_gaps>1</Hsp_gaps>
+      <Hsp_align-len>342</Hsp_align-len>
+      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE</Hsp_qseq>
+      <Hsp_hseq>MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE</Hsp_hseq>
+      <Hsp_midline>MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>29</Statistics_hsp-len>
+      <Statistics_eff-space>101761</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>21</Iteration_iter-num>
+  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>348</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gi|283855846|gb|ADB45242.1|</Hit_id>
+  <Hit_def>rhodopsin [Cynopterus brachyotis]</Hit_def>
+  <Hit_accession>ADB45242</Hit_accession>
+  <Hit_len>328</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>653.284</Hsp_bit-score>
+      <Hsp_score>1684</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>11</Hsp_query-from>
+      <Hsp_query-to>338</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>328</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>311</Hsp_identity>
+      <Hsp_positive>321</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>328</Hsp_align-len>
+      <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq>
+      <Hsp_hseq>VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq>
+      <Hsp_midline>VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>29</Statistics_hsp-len>
+      <Statistics_eff-space>101761</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>22</Iteration_iter-num>
+  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>348</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gi|283855823|gb|ADB45229.1|</Hit_id>
+  <Hit_def>rhodopsin [Myotis pilosus]</Hit_def>
+  <Hit_accession>ADB45229</Hit_accession>
+  <Hit_len>328</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>631.328</Hsp_bit-score>
+      <Hsp_score>1627</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>11</Hsp_query-from>
+      <Hsp_query-to>338</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>328</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>311</Hsp_identity>
+      <Hsp_positive>323</Hsp_positive>
+      <Hsp_gaps>0</Hsp_gaps>
+      <Hsp_align-len>328</Hsp_align-len>
+      <Hsp_qseq>VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS</Hsp_qseq>
+      <Hsp_hseq>VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS</Hsp_hseq>
+      <Hsp_midline>VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>29</Statistics_hsp-len>
+      <Statistics_eff-space>101761</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>23</Iteration_iter-num>
+  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>348</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gi|223523|prf||0811197A</Hit_id>
+  <Hit_def>rhodopsin [Bos taurus]</Hit_def>
+  <Hit_accession>0811197A</Hit_accession>
+  <Hit_len>347</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>673.315</Hsp_bit-score>
+      <Hsp_score>1736</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>348</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>347</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>324</Hsp_identity>
+      <Hsp_positive>336</Hsp_positive>
+      <Hsp_gaps>1</Hsp_gaps>
+      <Hsp_align-len>348</Hsp_align-len>
+      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>
+      <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>
+      <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>29</Statistics_hsp-len>
+      <Statistics_eff-space>101761</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+<Iteration>
+  <Iteration_iter-num>24</Iteration_iter-num>
+  <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>
+  <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>
+  <Iteration_query-len>348</Iteration_query-len>
+<Iteration_hits>
+<Hit>
+  <Hit_num>1</Hit_num>
+  <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id>
+  <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def>
+  <Hit_accession>BAB21486</Hit_accession>
+  <Hit_len>354</Hit_len>
+  <Hit_hsps>
+    <Hsp>
+      <Hsp_num>1</Hsp_num>
+      <Hsp_bit-score>599.356</Hsp_bit-score>
+      <Hsp_score>1544</Hsp_score>
+      <Hsp_evalue>0</Hsp_evalue>
+      <Hsp_query-from>1</Hsp_query-from>
+      <Hsp_query-to>341</Hsp_query-to>
+      <Hsp_hit-from>1</Hsp_hit-from>
+      <Hsp_hit-to>342</Hsp_hit-to>
+      <Hsp_query-frame>0</Hsp_query-frame>
+      <Hsp_hit-frame>0</Hsp_hit-frame>
+      <Hsp_identity>281</Hsp_identity>
+      <Hsp_positive>314</Hsp_positive>
+      <Hsp_gaps>1</Hsp_gaps>
+      <Hsp_align-len>342</Hsp_align-len>
+      <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>
+      <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>
+      <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV  TW MALACA PPL GWSRYIPEGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP   +D ASAT SKTE</Hsp_midline>
+    </Hsp>
+  </Hit_hsps>
+</Hit>
+</Iteration_hits>
+  <Iteration_stat>
+    <Statistics>
+      <Statistics_db-num>0</Statistics_db-num>
+      <Statistics_db-len>0</Statistics_db-len>
+      <Statistics_hsp-len>29</Statistics_hsp-len>
+      <Statistics_eff-space>101761</Statistics_eff-space>
+      <Statistics_kappa>0.041</Statistics_kappa>
+      <Statistics_lambda>0.267</Statistics_lambda>
+      <Statistics_entropy>0.14</Statistics_entropy>
+    </Statistics>
+  </Iteration_stat>
+</Iteration>
+</BlastOutput_iterations>
+</BlastOutput>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular	Fri Jun 13 07:07:35 2014 -0400
@@ -0,0 +1,6 @@
+sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1|	96.55	348	12	0	1	348	1	348	0.0	701	gi|57163783|ref|NP_001009242.1|	1808	336	343	0	98.56	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA	348	348	rhodopsin [Felis catus]
+sp|P08100|OPSD_HUMAN	gi|3024260|sp|P56514.1|OPSD_BUFBU	84.80	342	51	1	1	341	1	342	0.0	619	gi|3024260|sp|P56514.1|OPSD_BUFBU	1595	290	322	1	94.15	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE	MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE	348	354	RecName: Full=Rhodopsin
+sp|P08100|OPSD_HUMAN	gi|283855846|gb|ADB45242.1|	94.82	328	17	0	11	338	1	328	0.0	653	gi|283855846|gb|ADB45242.1|	1684	311	321	0	97.87	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328	rhodopsin [Cynopterus brachyotis]
+sp|P08100|OPSD_HUMAN	gi|283855823|gb|ADB45229.1|	94.82	328	17	0	11	338	1	328	0.0	631	gi|283855823|gb|ADB45229.1|	1627	311	323	0	98.48	1	1	VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS	VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS	348	328	rhodopsin [Myotis pilosus]
+sp|P08100|OPSD_HUMAN	gi|223523|prf||0811197A	93.10	348	23	1	1	348	1	347	0.0	673	gi|223523|prf||0811197A	1736	324	336	1	96.55	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA	MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA	348	347	rhodopsin [Bos taurus]
+sp|P08100|OPSD_HUMAN	gi|12583665|dbj|BAB21486.1|	82.16	342	60	1	1	341	1	342	0.0	599	gi|12583665|dbj|BAB21486.1|	1544	281	314	1	91.81	1	1	MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE	MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE	348	354	fresh water form rod opsin [Conger myriaster]
--- a/test-data/blastp_four_human_vs_rhodopsin_top3.tabular	Wed Sep 18 06:07:53 2013 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin_top3.tabular	Fri Jun 13 07:07:35 2014 -0400
@@ -1,25 +1,5 @@
 #Query	BLAST hit 1	BLAST hit 2	BLAST hit 3
 sp|Q9BS26|ERP44_HUMAN			
-sp|Q9BS26|ERP44_HUMAN			
-sp|Q9BS26|ERP44_HUMAN			
-sp|Q9BS26|ERP44_HUMAN			
-sp|Q9BS26|ERP44_HUMAN			
-sp|Q9BS26|ERP44_HUMAN			
 sp|Q9NSY1|BMP2K_HUMAN			
-sp|Q9NSY1|BMP2K_HUMAN			
-sp|Q9NSY1|BMP2K_HUMAN			
-sp|Q9NSY1|BMP2K_HUMAN			
-sp|Q9NSY1|BMP2K_HUMAN			
-sp|Q9NSY1|BMP2K_HUMAN			
 sp|P06213|INSR_HUMAN			
-sp|P06213|INSR_HUMAN			
-sp|P06213|INSR_HUMAN			
-sp|P06213|INSR_HUMAN			
-sp|P06213|INSR_HUMAN			
-sp|P06213|INSR_HUMAN			
-sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]		
-sp|P08100|OPSD_HUMAN	gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin		
-sp|P08100|OPSD_HUMAN	gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis]		
-sp|P08100|OPSD_HUMAN	gi|283855823|gb|ADB45229.1| rhodopsin [Myotis pilosus]		
-sp|P08100|OPSD_HUMAN	gi|223523|prf||0811197A rhodopsin [Bos taurus]		
-sp|P08100|OPSD_HUMAN	gi|12583665|dbj|BAB21486.1| fresh water form rod opsin [Conger myriaster]		
+sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]	gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin	gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis]
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular	Fri Jun 13 07:07:35 2014 -0400
@@ -0,0 +1,2 @@
+#Query	BLAST hit 1	BLAST hit 2	BLAST hit 3
+sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]	gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin	gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis]
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blastxml_to_top_descr/README.rst	Fri Jun 13 07:07:35 2014 -0400
@@ -0,0 +1,128 @@
+Galaxy tool to extract top BLAST hit descriptions from BLAST XML
+================================================================
+
+This tool is copyright 2012-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This tool is a short Python script to parse a BLAST XML file, and extract the
+identifiers with description for the top matches (by default the top 3), and
+output these as a simple tabular file along with the query identifiers.
+
+It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
+
+This requires the 'blast_datatypes' repository from the Galaxy Tool Shed
+to provide the 'blastxml' file format definition.
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically install the
+'blast_datatypes' dependency.
+
+
+Manual Installation
+===================
+
+If you haven't done so before, first install the 'blast_datatypes' repository.
+
+There are just two files to install (if doing this manually):
+
+* blastxml_to_top_descr.py (the Python script)
+* blastxml_to_top_descr.xml (the Galaxy tool definition)
+
+The suggested location is in the Galaxy folder tools/ncbi_blast_plus next to
+the NCBI BLAST+ tool wrappers.
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer
+the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line::
+
+    <tool file="ncbi_blast_plus/blastxml_to_top_descr.xml" />
+
+To run the tool's tests, also add this line to tools_conf.xml.sample then::
+
+    $ sh run_functional_tests.sh -id blastxml_to_top_descr
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version.
+v0.0.2  - Since BLAST+ was moved out of the Galaxy core, now have a dependency
+          on the 'blast_datatypes' repository in the Tool Shed.
+v0.0.3  - Include the test files required to run the unit tests
+v0.0.4  - Quote filenames in case they contain spaces (internal change)
+v0.0.5  - Include number of queries with BLAST matches in stdout (peek text)
+v0.0.6  - Check for errors via the script's return code (internal change)
+v0.0.7  - Link to Tool Shed added to help text and this documentation.
+        - Tweak dependency on blast_datatypes to also work on Test Tool Shed
+        - Adopt standard MIT License.
+v0.0.8  - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
+v0.0.9  - Updated citation information (Cock et al. 2013).
+v0.0.10 - Update help text to mention BLAST+ 2.2.28 can produce tabular files
+          including the description/title (via the salltitles field).
+v0.1.0  - Switch to using an optparse based API for Python script internally.
+        - Support BLAST XML with multiple ``<Iteration>`` blocks per query.
+        - Support the default 25 column extended tabular BLAST output.
+======= ======================================================================
+
+
+Bug Reports
+===========
+
+You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
+us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
+
+
+Developers
+==========
+
+This script and related tools were originally developed on the 'tools' branch of
+the following Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/
+
+As of July 2013, development is continuing on a dedicated GitHub repository:
+https://github.com/peterjc/galaxy_blast
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the GitHub repository root folder::
+
+    $ tar -czf blastxml_to_top_descr.tar.gz tools/blastxml_to_top_descr/README.rst tools/blastxml_to_top_descr/blastxml_to_top_descr.* tools/blastxml_to_top_descr/repository_dependencies.xml test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastp_four_human_vs_rhodopsin_top3.tabular test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular
+
+Check this worked::
+
+    $ tar -tzf blastxml_to_top_descr.tar.gz
+    tools/blastxml_to_top_descr/README.rst
+    tools/blastxml_to_top_descr/blastxml_to_top_descr.py
+    tools/blastxml_to_top_descr/blastxml_to_top_descr.xml
+    tools/blastxml_to_top_descr/repository_dependencies.xml
+    test-data/blastp_four_human_vs_rhodopsin.xml
+    test-data/blastp_four_human_vs_rhodopsin_top3.tabular
+    test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular
+    test-data/blastp_four_human_vs_rhodopsin_top3_positive.tabular
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.py	Fri Jun 13 07:07:35 2014 -0400
@@ -0,0 +1,255 @@
+#!/usr/bin/env python
+"""Convert a BLAST XML file to a top hits description table.
+
+Takes three command line options, input BLAST XML filename, output tabular
+BLAST filename, number of hits to collect the descriptions of.
+
+Assumes the hits are pre-sorted, so "best" 3 hits gives first 3 hits.
+"""
+import os
+import sys
+import re
+from optparse import OptionParser
+
+if "-v" in sys.argv or "--version" in sys.argv:
+    print "v0.1.0"
+    sys.exit(0)
+
+if sys.version_info[:2] >= ( 2, 5 ):
+    import xml.etree.cElementTree as ElementTree
+else:
+    from galaxy import eggs
+    import pkg_resources; pkg_resources.require( "elementtree" )
+    from elementtree import ElementTree
+
+def stop_err( msg ):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(1)
+
+usage = """Use as follows:
+
+$ blastxml_to_top_descr.py [-t 3] -o example.tabular input.xml
+
+Or,
+
+$ blastxml_to_top_descr.py [--topN 3] --output example.tabular input.xml
+
+This will take the top 3 BLAST descriptions from the input BLAST XML file,
+writing them to the specified output file in tabular format.
+"""
+
+parser = OptionParser(usage=usage)
+parser.add_option("-t", "--topN", dest="topN", default=3,
+                  help="Number of descriptions to collect (in order from file)")
+parser.add_option("-o", "--output", dest="out_file", default=None,
+                  help="Output filename for tabular file",
+                  metavar="FILE")
+parser.add_option("-f", "--format", dest="format", default="blastxml",
+                  help="Input format (blastxml or tabular)")
+parser.add_option("-q", "--qseqid", dest="qseqid", default="1",
+                  help="Column for query 'qseqid' (for tabular input; default 1)")
+parser.add_option("-s", "--sseqid", dest="sseqid", default="2",
+                  help="Column for subject 'sseqid' (for tabular input; default 2)")
+parser.add_option("-d", "--salltitles", dest="salltitles", default="25",
+                  help="Column for descriptions 'salltitles' (for tabular input; default 25)")
+(options, args) = parser.parse_args()
+
+if len(sys.argv) == 4 and len(args) == 3 and not options.out_file:
+    stop_err("""The API has changed, replace this:
+
+$ python blastxml_to_top_descr.py input.xml output.tab 3
+
+with:
+
+$ python blastxml_to_top_descr.py -o output.tab -t 3 input.xml
+
+Sorry.
+""")
+
+if not args:
+    stop_err("Input filename missing, try -h")
+if len(args) > 1:
+    stop_err("Expects a single argument, one input filename")
+in_file = args[0]
+out_file = options.out_file
+topN = options.topN
+
+try:
+    topN = int(topN)
+except ValueError:
+    stop_err("Number of hits  argument should be an integer (at least 1)")
+if topN < 1:
+    stop_err("Number of hits  argument should be an integer (at least 1)")
+
+if not os.path.isfile(in_file):
+    stop_err("Missing input file: %r" % in_file)
+
+
+def get_column(value):
+    """Convert column number on command line to Python index."""
+    if value.startswith("c"):
+        # Ignore c prefix, e.g. "c1" for "1"
+        value = value[1:]
+    try:
+        col = int(value)
+    except:
+        stop_err("Expected an integer column number, not %r" % value)
+    if col < 1:
+        stop_err("Expect column numbers to be at least one, not %r" % value)
+    return col - 1 # Python counting!
+
+def tabular_hits(in_file, qseqid, sseqid, salltitles):
+    """Parse key data from tabular BLAST output.
+
+    Iterator returning tuples (qseqid, list_of_subject_description)
+    """
+    current_query = None
+    current_hits = []
+    with open(in_file) as input:
+        for line in input:
+            parts = line.rstrip("\n").split("\t")
+            query = parts[qseqid]
+            descr = "%s %s" % (parts[sseqid], parts[salltitles])
+            if current_query is None:
+                # First hit
+                current_query = query
+                current_hits = [descr]
+            elif current_query == query:
+                # Another hit
+                current_hits.append(descr)
+            else:
+                # New query
+                yield current_query, current_hits
+                current_query = query
+                current_hits = [descr]
+    if current_query is not None:
+        # Final query
+        yield current_query, current_hits
+
+def blastxml_hits(in_file):
+    """Parse key data from BLAST XML output.
+
+    Iterator returning tuples (qseqid, list_of_subject_description)
+    """
+    try:
+        context = ElementTree.iterparse(in_file, events=("start", "end"))
+    except:
+        with open(in_file) as handle:
+            header = handle.read(100)
+        stop_err("Invalid data format in XML file %r which starts: %r" % (in_file, header))
+    # turn it into an iterator
+    context = iter(context)
+    # get the root element
+    try:
+        event, root = context.next()
+    except:
+        with open(in_file) as handle:
+            header = handle.read(100)
+        stop_err("Unable to get root element from XML file %r which starts: %r" % (in_file, header))
+
+    re_default_query_id = re.compile("^Query_\d+$")
+    assert re_default_query_id.match("Query_101")
+    assert not re_default_query_id.match("Query_101a")
+    assert not re_default_query_id.match("MyQuery_101")
+    re_default_subject_id = re.compile("^Subject_\d+$")
+    assert re_default_subject_id.match("Subject_1")
+    assert not re_default_subject_id.match("Subject_")
+    assert not re_default_subject_id.match("Subject_12a")
+    assert not re_default_subject_id.match("TheSubject_1")
+
+    count = 0
+    pos_count = 0
+    current_query = None
+    hit_descrs = []
+    for event, elem in context:
+        # for every <Iteration> tag
+        if event == "end" and elem.tag == "Iteration":
+            # Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA
+            # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>
+            # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>
+            # <Iteration_query-len>406</Iteration_query-len>
+            # <Iteration_hits></Iteration_hits>
+            #
+            # Or, from BLAST 2.2.24+ run online
+            # <Iteration_query-ID>Query_1</Iteration_query-ID>
+            # <Iteration_query-def>Sample</Iteration_query-def>
+            # <Iteration_query-len>516</Iteration_query-len>
+            # <Iteration_hits>...
+            qseqid = elem.findtext("Iteration_query-ID")
+            if qseqid is None:
+                stop_err("Missing <Iteration_query-ID> (could be really old BLAST XML data?)")
+            if re_default_query_id.match(qseqid):
+                #Place holder ID, take the first word of the query definition
+                qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
+            if current_query is None:
+                # First hit
+                current_query = qseqid
+                hit_descrs = []
+            elif current_query != qseqid:
+                # New hit
+                yield current_query, hit_descrs
+                current_query = qseqid
+                hit_descrs = []
+            else:
+                # Continuation of previous query
+                # i.e. This BLAST XML did not use one <Iteration> per query
+                # sys.stderr.write("Multiple <Iteration> blocks for %s\n" % qseqid)
+                pass
+            # for every <Hit> within <Iteration>
+            for hit in elem.findall("Iteration_hits/Hit"):
+                # Expecting either this,
+                # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id>
+                # <Hit_def>RecName: Full=Rhodopsin</Hit_def>
+                # <Hit_accession>P56514</Hit_accession>
+                # or,
+                # <Hit_id>Subject_1</Hit_id>
+                # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def>
+                # <Hit_accession>Subject_1</Hit_accession>
+                #
+                #apparently depending on the parse_deflines switch
+                sseqid = hit.findtext("Hit_id").split(None,1)[0]
+                hit_def = sseqid + " " + hit.findtext("Hit_def")
+                if re_default_subject_id.match(sseqid) \
+                and sseqid == hit.findtext("Hit_accession"):
+                    #Place holder ID, take the first word of the subject definition
+                    hit_def = hit.findtext("Hit_def")
+                    sseqid = hit_def.split(None,1)[0]
+                assert hit_def not in hit_descrs
+                hit_descrs.append(hit_def)
+            # prevents ElementTree from growing large datastructure
+            root.clear()
+            elem.clear()
+    if current_query is not None:
+        # Final query
+        yield current_query, hit_descrs
+
+if options.format == "blastxml":
+    hits = blastxml_hits(in_file)
+elif options.format == "tabular":
+    qseqid = get_column(options.qseqid)
+    sseqid = get_column(options.sseqid)
+    salltitles = get_column(options.salltitles)
+    hits = tabular_hits(in_file, qseqid, sseqid, salltitles)
+else:
+    stop_err("Unsupported format: %r" % options.format)
+
+
+def best_hits(descriptions, topN):
+    if len(descriptions) < topN:
+        return descriptions +  [""] * (topN - len(descriptions))
+    else:
+        return descriptions[:topN]
+
+count = 0
+if out_file is None:
+    outfile = sys.stdout
+else:
+    outfile = open(out_file, 'w')
+outfile.write("#Query\t%s\n" % "\t".join("BLAST hit %i" % (i+1) for i in range(topN)))
+for query, descrs in hits:
+    count += 1
+    outfile.write("%s\t%s\n" % (query, "\t".join(best_hits(descrs, topN))))
+if out_file is not None:
+    outfile.close()
+# Queries with no hits are not present in tabular BLAST output
+print("%i queries with BLAST results" % count)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml	Fri Jun 13 07:07:35 2014 -0400
@@ -0,0 +1,111 @@
+<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.0">
+    <description>Make a table from BLAST output</description>
+    <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command>
+    <command interpreter="python">
+blastxml_to_top_descr.py
+-f "$input.in_format"
+#if $input.in_format == "tabular":
+    --qseqid $input.qseqid
+    --sseqid $input.sseqid
+    --salltitles $input.salltitles
+#end if
+-o "${tabular_file}"
+-t ${topN}
+"${in_file}"
+    </command>
+    <stdio>
+        <!-- Assume anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <conditional name="input">
+            <param name="in_format" type="select" label="Input format">
+                <option value="blastxml" select="True">BLAST XML</option>
+                <option value="tabular">Tabular</option>
+            </param>
+            <when value="blastxml">
+                <param name="in_file" type="data" format="blastxml" label="BLAST results as XML"/>
+            </when>
+            <when value="tabular">
+                <param name="in_file" type="data" format="tabular" label="BLAST results as tabular"/>
+                <param name="qseqid" type="data_column" data_ref="in_file"
+		       multiple="False" numerical="False" default_value="1" value="1"
+		       label="Column containing query ID (qseqid)"
+		       help="This is column 1 in standard BLAST tabular output" />
+		<param name="sseqid" type="data_column" data_ref="in_file"
+		       multiple="False" numerical="False" default_value="2" value="2"
+		       label="Column containing match ID (sseqid)"
+		       help="This is column 2 in standard BLAST tabular output"/>
+                <param name="salltitles" type="data_column" data_ref="in_file"
+		       multiple="False" numerical="False" default_value="25" value="25"
+                       label="Column containing containing descriptions (salltitles)"
+		       help="This is column 25 in the default extended BLAST tabular output"/>
+            </when>
+        </conditional>
+        <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/>
+    </inputs>
+    <outputs>
+        <data name="tabular_file" format="tabular" label="Top $topN descriptions from $input.in_file.name" />
+    </outputs>
+    <requirements>
+    </requirements>
+    <tests>
+        <test>
+            <param name="in_format" value="blastxml" />
+            <param name="in_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
+            <param name="topN" value="3" />
+            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="in_format" value="tabular" />
+            <param name="in_file" value="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" />
+            <param name="topN" value="3" />
+            <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3_positive.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
+formats including text, tabular and a more detailed XML format. You can
+do a lot of things with tabular files in Galaxy (sorting, filtering, joins,
+etc), however until BLAST+ 2.2.28 the tabular output never included the
+hit descriptions (titles) found in the other output formats.
+
+This tool turns a BLAST XML file into a simple tabular file containing
+one row per query sequence, containing the query identifier and then
+the three (by default) top hit descriptions (i.e. the first three). If
+a query doesn't have that many hits, then these entries are left blank.
+
+This tool can also be used with the tabular output from BLAST+ instead,
+provided the relevant columns are provided. The default settings will
+work with the default 25 column extended output from the BLAST+ tools
+wrapped in Galaxy. Note if a query has *no* hits, it does not appear in
+the BLAST tabular output.
+
+**Example Usage**
+
+One simple usage would be to take a transcriptome assembly or set of
+gene predictions, run a BLAST search against the NCBI NR database, and
+then use this tool to make a table of the top three BLAST hits. This
+can give you a 'quick and dirty' crude annotation, potentially enough
+to spot some problems (e.g. bacterial contaimination could be very
+obvious).
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blastxml_to_top_descr/repository_dependencies.xml	Fri Jun 13 07:07:35 2014 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Requires BLAST XML and database datatype definitions.">
+<repository changeset_revision="de11e1a921c4" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>