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comparison interproscan.xml @ 4:fcedfe919603 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"
author iuc
date Mon, 15 Nov 2021 17:53:24 +0000
parents 52f20362d488
children 2e1cf7d85dbc
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3:8ee90fc5fe11 4:fcedfe919603
1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.2"> 1 <tool id="interproscan" name="InterProScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
2 <description>Interproscan functional predictions of ORFs</description> 2 <description>functional annotation</description>
3 <command> 3 <macros>
4 ## The command is a Cheetah template which allows some Python based syntax. 4 <import>macros.xml</import>
5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces 5 </macros>
6 6 <xrefs>
7 ## create temp directory 7 <xref type="bio.tools">interproscan_4</xref>
8 #import tempfile, os 8 </xrefs>
9 #set $tfile = tempfile.mkstemp()[1] 9 <requirements>
10 10 <requirement type="package" version="@TOOL_VERSION@">interproscan</requirement>
11 sed 's/ /_/g' $input > $tfile; 11 </requirements>
12 12 <version_command>interproscan.sh --version</version_command>
13 ## Hack, because interproscan does not seem to produce gff output even if it is configured 13 <command><![CDATA[
14 #if str($oformat) == "gff": 14 ## Adapt properties file to use data from data table
15 #set $tfile2 = tempfile.mkstemp()[1] 15 mkdir -p \$HOME/.interproscan-5
16 iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl 2>&#38;1; 16 &&
17 converter.pl -format gff3 -input $tfile2 -output $output; 17 sed 's|^\(data.directory=\).*$|\1${database.fields.path}|' \$(dirname \$(readlink -f \$(command -v interproscan.sh)))/interproscan.properties > \$HOME/.interproscan-5/interproscan.properties
18 rm $tfile2; 18 &&
19 #else 19
20 iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl 2>&#38;1; 20 ## Now run interproscan
21 interproscan.sh
22
23 ## disables the precalculated lookup service, all calculation will be run locally
24 -dp
25 --input '$input'
26 --seqtype $seqtype
27 -f ${','.join($oformat)}
28
29 #if $licensed.use == 'true' and $licensed.applications_licensed:
30 --applications ${','.join($applications)},${','.join($licensed.applications_licensed)}
31 #else:
32 --applications ${','.join($applications)}
21 #end if 33 #end if
22 34 --tempdir \$TEMP
23 rm $tfile 35
24 36 $pathways
25 </command> 37 $goterms
26 <inputs> 38 $iprlookup
27 <param name="input" type="data" format="fasta" label="Protein Fasta File"/> 39
28 40 --cpu \${GALAXY_SLOTS:-4}
29 <param name="appl" type="select" format="text" label="Applications to run" help="Select your programm."> 41
30 <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option> 42 --output-file-base 'output'
31 <option value="seg">seg</option> 43 ]]></command>
32 <option value="signalp">signalp</option> 44 <inputs>
33 <option value="tmhmm">tmhmm</option> 45 <param argument="--input" type="data" format="fasta" label="Protein FASTA File"/>
34 <option value="fprintscan">fprintscan</option> 46
35 <option value="patternscan">patternscan</option> 47 <param argument="--seqtype" type="select" label="Type of the input sequences" help="">
36 <option value="profilescan">profilescan</option> 48 <option value="p" selected="true">Protein</option>
37 <option value="superfamily">superfamily</option> 49 <option value="n">DNA / RNA</option>
38 <option value="hmmpir">hmmpir</option> 50 </param>
39 <option value="hmmpfam">hmmpfam</option> 51
40 <option value="hmmsmart">hmmsmart</option> 52 <param name="database" label="InterProScan database" type="select">
41 <option value="hmmtigr">hmmtigr</option> 53 <options from_data_table="interproscan">
42 <option value="hmmpanther">hmmpanther</option> 54 <column name="value" index="0" />
43 <option value="hamap">hamap</option> 55 <column name="name" index="1" />
44 <option value="gene3d">gene3d</option> 56 <column name="path" index="3" />
45 <option value="coils">coils</option> 57 <filter type="sort_by" column="0" />
46 <option value="blastprodom">blastprodom</option> 58 <filter type="static_value" column="2" value="@TOOL_VERSION@" />
59 </options>
60 </param>
61
62 <param name="applications" type="select" multiple="True" label="Applications to run" help="Select your program">
63 <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on hidden Markov models (HMMs)</option>
64 <option value="SFLD" selected="true">SFLD: a database of protein families based on hidden Markov models (HMMs)</option>
65 <option value="SUPERFAMILY" selected="true">SUPERFAMILY: database of structural and functional annotation for all proteins and genomes</option>
66 <option value="PANTHER" selected="true">PANTHER: Protein ANalysis THrough Evolutionary Relationships</option>
67 <option value="Gene3D" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
68 <option value="Hamap" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
69 <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>
70 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
71 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
72 <option value="CDD" selected="true">SMART: protein domains and families based on well-annotated multiple sequence alignment models</option>
73 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
74 <option value="PIRSR" selected="true">PIRSR: protein families based on hidden Markov models (HMMs) and Site Rules</option>
75 <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>
76 <option value="Pfam" selected="true">Pfam: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
77 <option value="MobiDBLite" selected="true">MobiDBLite: Prediction of intrinsically disordered regions in proteins</option>
78 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
79 </param>
80
81 <conditional name="licensed">
82 <param name="use" type="select" label="Use applications with restricted license, only for non-commercial use?" help="The corresponding tools must be installed manually by the administrator of this Galaxy instance" >
83 <option value="false" selected="true">No</option>
84 <option value="true">Yes</option>
47 </param> 85 </param>
48 86 <when value="false" />
49 <param name="oformat" type="select" label="Output format" help="Please select a output format."> 87 <when value="true">
50 <option value="gff">gff</option> 88 <param name="applications_licensed" type="select" multiple="True" label="Applications to run" help="Select your programm.">
51 <option value="raw" selected="true">raw</option> 89 <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide predictor</option>
52 <option value="txt">txt</option> 90 <option value="SignalP_GRAM_NEGATIVE" selected="false">SignalP (gram-negative): signal peptide cleavage sites in amino acid sequences for gram-negative prokaryotes</option>
53 <option value="html">html</option> 91 <option value="SignalP_EUK" selected="true">SignalP (eukaryotes): signal peptide cleavage sites in amino acid sequences for eukaryotes</option>
54 <option value="xml">xml</option> 92 <option value="SignalP_GRAM_POSITIVE" selected="false">SignalP (Gram Positive Bacteria): signal peptide cleavage sites in amino acid sequences for gram-positive prokaryotes</option>
55 <option value="ebixml">EBI header on top of xml</option> 93 <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option>
56 </param> 94 </param>
57 95 </when>
58 </inputs> 96 </conditional>
97
98 <param argument="--pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean" label="Include pathway information"
99 help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries."/>
100 <param argument="--goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings"
101 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option."/>
102 <param argument="--iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
103 label="Provide additional mappings" help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into"/>
104
105 <param name="oformat" type="select" multiple="true" label="Output format" help="Please select a output format (JSON output can be visualised on https://www.ebi.ac.uk/interpro/result/InterProScan/).">
106 <option value="TSV" selected="true">Tab-separated values format (TSV)</option>
107 <option value="GFF3">GFF3</option>
108 <option value="XML">XML</option>
109 <option value="JSON">JSON</option>
110 </param>
111 </inputs>
112
59 <outputs> 113 <outputs>
60 114 <data format="tabular" name="outfile_tsv" from_work_dir="output.tsv" label="InterProScan on ${on_string} (tsv)">
61 <data format="txt" name="output" label="Interproscan calculation on ${on_string}"> 115 <filter>oformat and 'TSV' in outputs</filter>
62 <change_format>
63 <when input="oformat" value="html" format="html"/>
64 <when input="oformat" value="xml" format="xml"/>
65 <when input="oformat" value="ebixml" format="xml"/>
66 <when input="oformat" value="gff" format="gff"/>
67 </change_format>
68 </data> 116 </data>
69 117 <data format="xml" name="outfile_xml" from_work_dir="output.xml" label="InterProScan on ${on_string} (xml)">
118 <filter>oformat and 'XML' in outputs</filter>
119 </data>
120 <data format="gff3" name="outfile_gff3" from_work_dir="output.gff3" label="InterProScan on ${on_string} (gff3)">
121 <filter>oformat and 'GFF3' in outputs</filter>
122 </data>
123 <data format="json" name="outfile_json" from_work_dir="output.json" label="InterProScan on ${on_string} (json)">
124 <filter>oformat and 'JSON' in outputs</filter>
125 </data>
70 </outputs> 126 </outputs>
71 <requirements> 127
72 </requirements> 128 <tests>
73 <help> 129 <test>
130 <param name="input" value="prots.fa" />
131 <param name="seqtype" value="p" />
132 <param name="database" value="5.52-86.0" />
133 <param name="applications" value="MobiDBLite" />
134 <param name="oformat" value="TSV" />
135 <output name="outfile_tsv">
136 <assert_contents>
137 <has_text text="FUN_000011-T1" />
138 <has_text text="ea9924e11f7decc417e8d9ed8b9c682e" />
139 <has_text text="FUN_000012-T1" />
140 <has_text text="01beedc2fbf8012cba37f0c0d39aa071" />
141 </assert_contents>
142 </output>
143 </test>
144 <test>
145 <param name="input" value="prots.fa" />
146 <param name="seqtype" value="p" />
147 <param name="database" value="5.52-86.0" />
148 <param name="applications" value="MobiDBLite" />
149 <param name="oformat" value="TSV,GFF3,XML,JSON" />
150 <output name="outfile_tsv">
151 <assert_contents>
152 <has_text text="FUN_000011-T1" />
153 <has_text text="ea9924e11f7decc417e8d9ed8b9c682e" />
154 <has_text text="FUN_000012-T1" />
155 <has_text text="01beedc2fbf8012cba37f0c0d39aa071" />
156 </assert_contents>
157 </output>
158 <output name="outfile_xml">
159 <assert_contents>
160 <has_text text="mobidblite-location" />
161 <has_text text="Polyampholyte" />
162 <has_text text="consensus disorder prediction" />
163 <has_text text="FUN_000011-T1 FUN_000011" />
164 </assert_contents>
165 </output>
166 <output name="outfile_gff3">
167 <assert_contents>
168 <has_text text="protein_match" />
169 <has_text text="ID=FUN_000011-T1;md5=" />
170 <has_text text="MobiDBLite" />
171 </assert_contents>
172 </output>
173 <output name="outfile_json">
174 <assert_contents>
175 <has_text text="signatureLibraryRelease" />
176 <has_text text="disorder_prediction" />
177 <has_text text="Polyampholyte" />
178 </assert_contents>
179 </output>
180 </test>
181 <test>
182 <param name="input" value="transcripts.fa" />
183 <param name="seqtype" value="n" />
184 <param name="database" value="5.52-86.0" />
185 <param name="applications" value="MobiDBLite" />
186 <param name="oformat" value="TSV,GFF3,XML,JSON" />
187 <output name="outfile_tsv">
188 <assert_contents>
189 <has_text text="FUN_000018-T1_orf336" />
190 <has_text text="0b28fe115d4cc09260b038b19fb0b21d" />
191 <has_text text="FUN_000012-T1_orf133" />
192 <has_text text="01beedc2fbf8012cba37f0c0d39aa071" />
193 </assert_contents>
194 </output>
195 <output name="outfile_xml">
196 <assert_contents>
197 <has_text text="mobidblite-location" />
198 <has_text text="Polyampholyte" />
199 <has_text text="consensus disorder prediction" />
200 <has_text text="orf355" />
201 </assert_contents>
202 </output>
203 <output name="outfile_gff3">
204 <assert_contents>
205 <has_text text="protein_match" />
206 <has_text text="ID=FUN_000012-T1;" />
207 <has_text text="MobiDBLite" />
208 </assert_contents>
209 </output>
210 <output name="outfile_json">
211 <assert_contents>
212 <has_text text="signatureLibraryRelease" />
213 <has_text text="disorder_prediction" />
214 <has_text text="Polyampholyte" />
215 </assert_contents>
216 </output>
217 </test>
218 <test expect_failure="true">
219 <param name="input" value="prots.fa" />
220 <param name="seqtype" value="p" />
221 <param name="database" value="5.52-86.0" />
222 <param name="applications" value="MobiDBLite" />
223 <conditional name="licensed">
224 <param name="use" value="true" />
225 <param name="applications_licensed" value="Phobius,TMHMM" />
226 </conditional>
227 <param name="oformat" value="TSV" />
228 <assert_stdout>
229 <!-- expected to be "deactivated" as they are not installed by default -->
230 <has_text text="Analysis Phobius does not exist or is deactivated" />
231 <has_text text="Analysis TMHMM does not exist or is deactivated" />
232 </assert_stdout>
233 </test>
234 </tests>
235
236 <help><![CDATA[
237
74 **What it does** 238 **What it does**
75 239
76 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases. 240 Interproscan is a batch tool to query the InterPro database. It provides annotations based on multiple searches of profile and other functional databases.
77 These include SCOP, CATH, PFAM and SUPERFAMILY. 241
242 Phobius (licensed software), SignalP, SMART (licensed components) and TMHMM use
243 licensed code and data provided by third parties. If you wish to run these
244 analyses it will be necessary for you to obtain a licence from the vendor and
245 configure the Galaxy server InterProScan installation to use them.
78 246
79 **Input** 247 **Input**
80 248
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. 249 Required is a FASTA file containing protein or nucleotide sequences.
82 250
83 **Output** 251 **Output**
84 252
85 Example for the raw format. 253 In this version of InterProScan, you can retrieve output in any of the following five formats:
86 The output will consist of a tabular file with 14 columns and can be easily concatenated or filtered. 254
87 255 * TSV: tab-separated values format
88 ====== ================================================================ ====================================================================== 256 * XML: XML format
89 column example description 257 * GFF: The GFF 3.0 format
90 ====== ================================================================ ====================================================================== 258 * JSON: A JSON representation of the protein matches that can be visualised on https://www.ebi.ac.uk/interpro/result/InterProScan/
91 c1 NF00181542 id of the input sequence 259
92 c2 27A9BBAC0587AB84 crc64 (checksum) of the protein sequence (supposed to be unique) 260 **Example Output**
93 c3 272 length of the sequence (in AA) 261
94 c4 HMMPIR anaysis method launched. 262
95 c5 PIRSF001424 database members entry for this match 263 ::
96 c6 Prephenate dehydratase database member description for the entry 264
97 c7 1 start of the domain match 265 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
98 c8 270 end of the domain match 266 P51587 14086411a2cdf1c4cba63020e1622579 3418 ProSiteProfiles PS50138 BRCA2 repeat profile. 1002 1036 0.0 T 18-03-2013 IPR002093 BRCA2 repeat GO:0005515|GO:0006302
99 c9 6.5e-141 evalue of the match (reported by member database method) 267 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
100 c10 T status of the match (T: true, ?: unknown) 268 ...
101 c11 06-Aug-2005 date of the run. 269
102 c12 IPR008237 corresponding InterPro entry (if iprlookup requested by the user) 270
103 c13 Prephenate dehydratase with ACT region description of the InterPro entry 271 The TSV format presents the match data in columns as follows:
104 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) GO (gene ontology) description for the InterPro entry 272
105 ====== ================================================================ ====================================================================== 273 - Protein Accession (e.g. P51587)
106 274 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
107 **Database updates** 275 - Sequence Length (e.g. 3418)
108 276 - Analysis (e.g. Pfam / PRINTS / Gene3D)
109 Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases. 277 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
110 278 - Signature Description (e.g. BRCA2 repeat profile)
111 ----- 279 - Start location
112 Tools 280 - Stop location
113 ----- 281 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
114 282 - Status - is the status of the match (T: true)
115 **PROSITE patterns** 283 - Date - is the date of the run
116 Some biologically significant amino acid patterns can be summarised in 284 - (InterProScan annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
117 the form of regular expressions. 285 - (InterProScan annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
118 ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk). 286 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
119 287 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
120 **PROSITE profiles** 288
121 There are a number of protein families as well as functional or 289
122 structural domains that cannot be detected using patterns due to their extreme 290 **Extensible Markup Language (XML)**
123 sequence divergence, so the use of techniques based on weight matrices 291
124 (also known as profiles) allows the detection of such proteins or domains. 292 XML representation of the matches - this is the richest form of the data. The XML Schema Definition (XSD) is available [http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5 here].
125 A profile is a table of position-specific amino acid weights and gap costs. 293
126 The profile structure used in PROSITE is similar to but slightly more general 294 **Generic Feature Format Version 3 (GFF3)**
127 (Bucher P. et al., 1996) than the one introduced by M. Gribskov and 295
128 co-workers. 296 The GFF3 format is a flat tab-delimited file, which is much richer then the TSV output format. It allows you to trace back from matches to predicted proteins and to nucleic acid sequences. It also contains a FASTA format representation of the predicted protein sequences and their matches. You will find a documentation of all the columns and attributes used on [https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md].
129 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch). 297
130 298 **Example Output**
131 **PRINTS** 299
132 The PRINTS database houses a collection of protein family fingerprints. 300
133 These are groups of motifs that together are diagnostically more 301 ::
134 powerful than single motifs by making use of the biological context inherent in a 302
135 multiple-motif method. The fingerprinting method arose from the need for 303 ##gff-version 3
136 a reliable technique for detecting members of large, highly divergent 304 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
137 protein super-families. 305 ##sequence-region AACH01000027 1 1347
138 FingerPRINTScan (Scordis P. et al., 1999). 306 ##seqid|source|type|start|end|score|strand|phase|attributes
139 307 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
140 **PFAM** 308 AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
141 Pfam is a database of protein domain families. Pfam contains curated 309 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
142 multiple sequence alignments for each family and corresponding hidden 310 AACH01000027 Pfam protein_match 84 314 1.2E-45 + . Name=PF00696;signature_desc=Amino acid kinase family;Target=null 84 314;status=T;ID=match$8_84_314;Ontology_term="GO:0008652";date=15-04-2013;Dbxref="InterPro:IPR001048","Reactome:REACT_13"
143 Markov models (HMMs) (Eddy S.R., 1998). 311 ##sequence-region 2
144 Profile hidden Markov models are statistical models of the primary 312 ...
145 structure consensus of a sequence family. The construction and use 313 >pep_AACH01000027_1_1347
146 of Pfam is tightly tied to the HMMER software package. 314 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
147 hmmpfam from the HMMER2.3.2 package (by Sean Eddy, 315 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
148 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). 316 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
149 317 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
150 **PRODOM** 318 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
151 ProDom is a database of protein domain families obtained by automated 319 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
152 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful 320 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
153 for analysing the domain arrangements of complex protein families and the 321 RSQKAKGVLIYRDDWISITPEIQLLFTEF
154 homology relationships in modular proteins. ProDom families are built by 322 ...
155 an automated process based on a recursive use of PSI-BLAST homology 323 >match$8_84_314
156 searches. 324 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
157 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr 325 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
158 and Yoann Beausse beausse@toulouse.inra.fr) 326 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
159 a wrapper on top of the Blast package (Altschul S.F. et al., 1997). 327 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
160 328
161 **SMART** 329 ]]></help>
162 SMART (a Simple Modular Architecture Research Tool) allows the 330
163 identification and annotation of genetically mobile domains and the 331 <expand macro="citations" />
164 analysis of domain architectures. These domains are extensively
165 annotated with respect to phyletic distributions, functional class, tertiary
166 structures and functionally important residues. SMART alignments are
167 optimised manually and following construction of corresponding hidden Markov models (HMMs).
168 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
169 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
170
171 **TIGRFAMs**
172 TIGRFAMs are a collection of protein families featuring curated multiple
173 sequence alignments, Hidden Markov Models (HMMs) and associated
174 information designed to support the automated functional identification
175 of proteins by sequence homology. Classification by equivalog family
176 (see below), where achievable, complements classification by orthologs,
177 superfamily, domain or motif. It provides the information best suited
178 for automatic assignment of specific functions to proteins from large
179 scale genome sequencing projects.
180 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
181 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
182
183 **PIR SuperFamily**
184 PIR SuperFamily (PIRSF) is a classification system based on evolutionary
185 relationship of whole proteins.
186 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
187 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
188
189 **SUPERFAMILY**
190 SUPERFAMILY is a library of profile hidden Markov models that represent
191 all proteins of known structure, based on SCOP.
192 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
193 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
194 Optionally, predictions for coiled-coil, signal peptide cleavage sites
195 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file for details).
196
197 **GENE3D**
198 Gene3D is supplementary to the CATH database. This protein sequence database
199 contains proteins from complete genomes which have been clustered into protein
200 families and annotated with CATH domains, Pfam domains and functional
201 information from KEGG, GO, COG, Affymetrix and STRINGS.
202 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
203 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
204
205 **PANTHER**
206 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
207 Classification System was designed to classify proteins (and their genes)
208 in order to facilitate high-throughput analysis.
209 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
210 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
211 and blastall from the Blast package (Altschul S.F. et al., 1997).
212
213 ----------
214 References
215 ----------
216
217 Zdobnov EM, Apweiler R (2001)
218 InterProScan an integration platform for the signature-recognition methods in InterPro.
219 Bioinformatics 17, 847-848.
220 http://dx.doi.org/10.1093/bioinformatics/17.9.847
221
222 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
223 InterProScan: protein domains identifier.
224 Nucleic Acids Research 33 (Web Server issue), W116-W120.
225 http://dx.doi.org/10.1093/nar/gki442
226
227 Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)
228 InterPro: the integrative protein signature database.
229 Nucleic Acids Research 37 (Database Issue), D224-228.
230 http://dx.doi.org/10.1093/nar/gkn785
231
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
237 **Galaxy Wrapper Author**::
238
239 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
240 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
241
242 </help>
243 </tool> 332 </tool>