Mercurial > repos > bgruening > iprscan

comparison interproscan.xml @ 3:a773b8eaccce draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 08 Oct 2013 10:22:00 -0400
parents 32ae2da3a3e4
children
comparison
equal deleted inserted replaced
2:32ae2da3a3e4 3:a773b8eaccce
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 tabular file in galaxy with 14 columns and can be easily concatenated or filtered. 86 The output will consist of a tabular file with 14 columns and can be easily concatenated or filtered.
87 87
88 ====== ================================================================ ====================================================================== 88 ====== ================================================================ ======================================================================
89 column example description 89 column example description
90 ====== ================================================================ ====================================================================== 90 ====== ================================================================ ======================================================================
91 c1 NF00181542 the id of the input sequence 91 c1 NF00181542 id of the input sequence
92 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)
93 c3 272 the length of the sequence (in AA) 93 c3 272 length of the sequence (in AA)
94 c4 HMMPIR the anaysis method launched. 94 c4 HMMPIR anaysis method launched.
95 c5 PIRSF001424 the database members entry for this match 95 c5 PIRSF001424 database members entry for this match
96 c6 Prephenate dehydratase the database member description for the entry 96 c6 Prephenate dehydratase database member description for the entry
97 c7 1 the start of the domain match 97 c7 1 start of the domain match
98 c8 270 the end of the domain match 98 c8 270 end of the domain match
99 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)
100 c10 T the status of the match (T: true, ?: unknown) 100 c10 T status of the match (T: true, ?: unknown)
101 c11 06-Aug-2005 the date of the run. 101 c11 06-Aug-2005 date of the run.
102 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user) 102 c12 IPR008237 corresponding InterPro entry (if iprlookup requested by the user)
103 c13 Prephenate dehydratase with ACT region the description of the InterPro entry 103 c13 Prephenate dehydratase with ACT region description of the InterPro entry
104 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
105 ====== ================================================================ ====================================================================== 105 ====== ================================================================ ======================================================================
106 106
107 **Database updates** 107 **Database updates**
108 108
109 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.
228 InterPro: the integrative protein signature database. 228 InterPro: the integrative protein signature database.
229 Nucleic Acids Research 37 (Database Issue), D224-228. 229 Nucleic Acids Research 37 (Database Issue), D224-228.
230 http://dx.doi.org/10.1093/nar/gkn785 230 http://dx.doi.org/10.1093/nar/gkn785
231 231
232 232
233 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
234 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan
235
236
233 **Galaxy Wrapper Author**:: 237 **Galaxy Wrapper Author**::
234 238
235 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg 239 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
236 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter 240 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
237 241