Mercurial > repos > jankanis > blast2html

annotate blast xml example2.xml @ 11:7660519f2dc9

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
proper layout for alignments, added some links
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 12 May 2014 13:55:04 +0200
parents bad241dc701f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
1 <?xml version="1.0"?>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
2 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
3 <BlastOutput>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
4 <BlastOutput_program>blastn</BlastOutput_program>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
5 <BlastOutput_version>BLASTN 2.2.28+</BlastOutput_version>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
6 <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>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
7 <BlastOutput_db>/share/BlastDB/nt</BlastOutput_db>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
8 <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
9 <BlastOutput_query-def>No definition line</BlastOutput_query-def>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
10 <BlastOutput_query-len>16</BlastOutput_query-len>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
11 <BlastOutput_param>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
12 <Parameters>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
13 <Parameters_expect>0.001</Parameters_expect>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
14 <Parameters_sc-match>2</Parameters_sc-match>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
15 <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
16 <Parameters_gap-open>5</Parameters_gap-open>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
17 <Parameters_gap-extend>2</Parameters_gap-extend>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
18 <Parameters_filter>L;m;</Parameters_filter>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
19 </Parameters>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
20 </BlastOutput_param>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
21 <BlastOutput_iterations>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
22 <Iteration>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
23 <Iteration_iter-num>1</Iteration_iter-num>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
24 <Iteration_query-ID>Query_1</Iteration_query-ID>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
25 <Iteration_query-def>No definition line</Iteration_query-def>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
26 <Iteration_query-len>16</Iteration_query-len>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
27 <Iteration_hits>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
28 </Iteration_hits>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
29 <Iteration_stat>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
30 <Statistics>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
31 <Statistics_db-num>28813188</Statistics_db-num>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
32 <Statistics_db-len>53027764389</Statistics_db-len>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
33 <Statistics_hsp-len>13</Statistics_hsp-len>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
34 <Statistics_eff-space>157959578835</Statistics_eff-space>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
35 <Statistics_kappa>0.41</Statistics_kappa>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
36 <Statistics_lambda>0.625</Statistics_lambda>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
37 <Statistics_entropy>0.78</Statistics_entropy>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
38 </Statistics>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
39 </Iteration_stat>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
40 <Iteration_message>No hits found</Iteration_message>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
41 </Iteration>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
42 </BlastOutput_iterations>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
43 </BlastOutput>
bad241dc701f add example input blast xml and output html page
Jan Kanis <jan.code@jankanis.nl>
parents:
diff changeset
44