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comparison interproscan.xml @ 2:52f20362d488 draft

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Again help updates.
author bgruening
date Wed, 10 Jul 2013 14:53:51 -0400
parents eb12db502d3c
children fcedfe919603
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1:eb12db502d3c 2:52f20362d488
81 Required is a FASTA file containing ORF predictions. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores ``_`` by this tool before running with Interproscan. 81 Required is a FASTA file containing ORF predictions. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores ``_`` by this tool before running with Interproscan.
82 82
83 **Output** 83 **Output**
84 84
85 Example for the raw format. 85 Example for the raw format.
86 The output will consist of a file in Interproscan raw format, a tabular file in galaxy with 14 columns. 86 The output will consist of a tabular file with 14 columns and can be easily concatenated or filtered.
87 This can be use to upload the data into a relational database or concatenation of different runs.
88 87
89 ====== ================================================================ ====================================================================== 88 ====== ================================================================ ======================================================================
90 column example description 89 column example description
91 ====== ================================================================ ====================================================================== 90 ====== ================================================================ ======================================================================
92 c1 NF00181542 the id of the input sequence 91 c1 NF00181542 id of the input sequence
93 c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique) 92 c2 27A9BBAC0587AB84 crc64 (checksum) of the protein sequence (supposed to be unique)
94 c3 272 the length of the sequence (in AA) 93 c3 272 length of the sequence (in AA)
95 c4 HMMPIR the anaysis method launched. 94 c4 HMMPIR anaysis method launched.
96 c5 PIRSF001424 the database members entry for this match 95 c5 PIRSF001424 database members entry for this match
97 c6 Prephenate dehydratase the database member description for the entry 96 c6 Prephenate dehydratase database member description for the entry
98 c7 1 the start of the domain match 97 c7 1 start of the domain match
99 c8 270 the end of the domain match 98 c8 270 end of the domain match
100 c9 6.5e-141 the evalue of the match (reported by member database method) 99 c9 6.5e-141 evalue of the match (reported by member database method)
101 c10 T the status of the match (T: true, ?: unknown) 100 c10 T status of the match (T: true, ?: unknown)
102 c11 06-Aug-2005 the date of the run. 101 c11 06-Aug-2005 date of the run.
103 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user) 102 c12 IPR008237 corresponding InterPro entry (if iprlookup requested by the user)
104 c13 Prephenate dehydratase with ACT region the description of the InterPro entry 103 c13 Prephenate dehydratase with ACT region description of the InterPro entry
105 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry 104 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) GO (gene ontology) description for the InterPro entry
106 ====== ================================================================ ====================================================================== 105 ====== ================================================================ ======================================================================
107 106
108 **Database updates** 107 **Database updates**
109 108
110 Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases. 109 Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases.