Mercurial > repos > bjoern-gruening > iprscan
comparison interproscan.xml @ 0:341830c8cd37
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author | bjoern-gruening |
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date | Tue, 24 Jan 2012 07:35:10 -0500 |
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children | 94745fda6aff |
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1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.1"> | |
2 <description>Interproscan functional predictions of ORFs</description> | |
3 <command> | |
4 ## The command is a Cheetah template which allows some Python based syntax. | |
5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | |
6 | |
7 ## create temp directory | |
8 #import tempfile, os | |
9 #set $tfile = tempfile.mkstemp()[1] | |
10 | |
11 sed 's/ /_/g' $input > $tfile; | |
12 | |
13 ## Hack, because interproscan does not seem to produce gff output even if it is configured | |
14 #if str($oformat)=="gff": | |
15 #set $tfile2 = tempfile.mkstemp()[1] | |
16 iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl > /dev/null 2> /dev/null; | |
17 converter.pl -format gff3 -input $tfile2 -output $output | |
18 rm $tfile2 | |
19 #else | |
20 iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl > /dev/null 2> /dev/null; | |
21 #end if | |
22 | |
23 rm $tfile; | |
24 | |
25 </command> | |
26 <inputs> | |
27 <param name="input" type="data" format="fasta" label="Protein Fasta File"/> | |
28 | |
29 <param name="appl" type="select" format="text" help="Select your programm."> | |
30 <label>Applications to run ...</label> | |
31 <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option> | |
32 <option value="seg">seg</option> | |
33 <option value="signalp">signalp</option> | |
34 <option value="tmhmm">tmhmm</option> | |
35 <option value="fprintscan">fprintscan</option> | |
36 <option value="patternscan">patternscan</option> | |
37 <option value="profilescan">profilescan</option> | |
38 <option value="superfamily">superfamily</option> | |
39 <option value="hmmpir">hmmpir</option> | |
40 <option value="hmmpfam">hmmpfam</option> | |
41 <option value="hmmsmart">hmmsmart</option> | |
42 <option value="hmmtigr">hmmtigr</option> | |
43 <option value="hmmpanther">hmmpanther</option> | |
44 <option value="hamap">hamap</option> | |
45 <option value="gene3d">gene3d</option> | |
46 <option value="coils">coils</option> | |
47 <option value="blastprodom">blastprodom</option> | |
48 </param> | |
49 | |
50 <param name="oformat" type="select" label="Output format" help="Please select a output format."> | |
51 <option value="gff" selected="true">gff</option> | |
52 <option value="raw">raw</option> | |
53 <option value="txt">txt</option> | |
54 <option value="html">html</option> | |
55 <option value="xml">xml</option> | |
56 <option value="ebixml">EBI header on top of xml</option> | |
57 </param> | |
58 | |
59 </inputs> | |
60 <outputs> | |
61 | |
62 <data format="txt" name="output" label="Interproscan calculation on ${on_string}"> | |
63 <change_format> | |
64 <when input="oformat" value="html" format="html"/> | |
65 <when input="oformat" value="xml" format="xml"/> | |
66 <when input="oformat" value="ebixml" format="xml"/> | |
67 <when input="oformat" value="gff" format="gff"/> | |
68 </change_format> | |
69 </data> | |
70 | |
71 </outputs> | |
72 <requirements> | |
73 </requirements> | |
74 <help> | |
75 | |
76 **What it does** | |
77 | |
78 | |
79 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases. | |
80 These include SCOP, CATH, PFAM and SUPERFAMILY. | |
81 | |
82 **Input** | |
83 A FASTA file containing ORF predictions is required. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores (_) by this tool before submission to Interproscan. | |
84 | |
85 **Output** | |
86 | |
87 Example for the raw format. | |
88 This is a basic tab delimited format useful for uploading the data into a relational database or concatenation of different runs. | |
89 is all on one line. | |
90 | |
91 ====== ================================================================ ====================================================================== | |
92 column example description | |
93 ====== ================================================================ ====================================================================== | |
94 c1 NF00181542 the id of the input sequence. | |
95 c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique). | |
96 c3 272 the length of the sequence (in AA). | |
97 c4 HMMPIR the anaysis method launched. | |
98 c5 PIRSF001424 the database members entry for this match. | |
99 c6 Prephenate dehydratase the database member description for the entry. | |
100 c7 1 the start of the domain match. | |
101 c8 270 the end of the domain match. | |
102 c9 6.5e-141 the evalue of the match (reported by member database method). | |
103 c10 T the status of the match (T: true, ?: unknown). | |
104 c11 06-Aug-2005 the date of the run. | |
105 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user). | |
106 c13 Prephenate dehydratase with ACT region the description of the InterPro entry. | |
107 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry. | |
108 ====== ================================================================ ====================================================================== | |
109 | |
110 | |
111 **Database updates** | |
112 | |
113 Typically these take place 2-3 times a year. | |
114 | |
115 | |
116 **Tools** | |
117 | |
118 PROSITE patterns | |
119 | |
120 :: | |
121 | |
122 Some biologically significant amino acid patterns can be summarised in | |
123 the form of regular expressions. | |
124 ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk), | |
125 | |
126 PROSITE profiles | |
127 | |
128 :: | |
129 | |
130 There are a number of protein families as well as functional or | |
131 structural domains that cannot be detected using patterns due to their extreme | |
132 sequence divergence, so the use of techniques based on weight matrices | |
133 (also known as profiles) allows the detection of such proteins or domains. | |
134 A profile is a table of position-specific amino acid weights and gap costs. | |
135 The profile structure used in PROSITE is similar to but slightly more general | |
136 (Bucher P. et al., 1996 [7]) than the one introduced by M. Gribskov and | |
137 co-workers. | |
138 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch). | |
139 | |
140 PRINTS | |
141 | |
142 :: | |
143 | |
144 The PRINTS database houses a collection of protein family fingerprints. | |
145 These are groups of motifs that together are diagnostically more | |
146 powerful than single motifs by making use of the biological context inherent in a | |
147 multiple-motif method. The fingerprinting method arose from the need for | |
148 a reliable technique for detecting members of large, highly divergent | |
149 protein super-families. | |
150 FingerPRINTScan (Scordis P. et al., 1999 [8]). | |
151 | |
152 PFAM | |
153 | |
154 :: | |
155 | |
156 Pfam is a database of protein domain families. Pfam contains curated | |
157 multiple sequence alignments for each family and corresponding hidden | |
158 Markov models (HMMs) (Eddy S.R., 1998 [9]). | |
159 Profile hidden Markov models are statistical models of the primary | |
160 structure consensus of a sequence family. The construction and use | |
161 of Pfam is tightly tied to the HMMER software package. | |
162 hmmpfam from the HMMER2.3.2 package (by Sean Eddy, | |
163 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). | |
164 | |
165 PRODOM | |
166 | |
167 :: | |
168 | |
169 | |
170 ProDom is a database of protein domain families obtained by automated | |
171 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful | |
172 for analysing the domain arrangements of complex protein families and the | |
173 homology relationships in modular proteins. ProDom families are built by | |
174 an automated process based on a recursive use of PSI-BLAST homology | |
175 searches. | |
176 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr | |
177 and Yoann Beausse beausse@toulouse.inra.fr) | |
178 a wrapper on top of the Blast package (Altschul S.F. et al., 1997 [10]). | |
179 | |
180 | |
181 SMART | |
182 | |
183 :: | |
184 | |
185 SMART (a Simple Modular Architecture Research Tool) allows the | |
186 identification and annotation of genetically mobile domains and the | |
187 analysis of domain architectures. These domains are extensively | |
188 annotated with respect to phyletic distributions, functional class, tertiary | |
189 structures and functionally important residues. SMART alignments are | |
190 optimised manually and following construction of corresponding hidden Markov models (HMMs). | |
191 hmmpfam from the HMMER2.3.2 package (by Sean Eddy, | |
192 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). | |
193 | |
194 | |
195 TIGRFAMs | |
196 | |
197 :: | |
198 | |
199 TIGRFAMs are a collection of protein families featuring curated multiple | |
200 sequence alignments, Hidden Markov Models (HMMs) and associated | |
201 information designed to support the automated functional identification | |
202 of proteins by sequence homology. Classification by equivalog family | |
203 (see below), where achievable, complements classification by orthologs, | |
204 superfamily, domain or motif. It provides the information best suited | |
205 for automatic assignment of specific functions to proteins from large | |
206 scale genome sequencing projects. | |
207 hmmpfam from the HMMER2.3.2 package (by Sean Eddy, | |
208 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). | |
209 | |
210 PIR SuperFamily | |
211 | |
212 :: | |
213 | |
214 PIR SuperFamily (PIRSF) is a classification system based on evolutionary | |
215 relationship of whole proteins. | |
216 hmmpfam from the HMMER2.3.2 package (by Sean Eddy, | |
217 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). | |
218 | |
219 SUPERFAMILY | |
220 | |
221 :: | |
222 | |
223 SUPERFAMILY is a library of profile hidden Markov models that represent | |
224 all proteins of known structure, based on SCOP. | |
225 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy, | |
226 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). | |
227 Optionally, predictions for coiled-coil, signal peptide cleavage sites | |
228 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file | |
229 for details). | |
230 | |
231 | |
232 GENE3D | |
233 | |
234 :: | |
235 | |
236 Gene3D is supplementary to the CATH database. This protein sequence database | |
237 contains proteins from complete genomes which have been clustered into protein | |
238 families and annotated with CATH domains, Pfam domains and functional | |
239 information from KEGG, GO, COG, Affymetrix and STRINGS. | |
240 hmmpfam from the HMM2.3.2 package (by Sean Eddy, | |
241 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). | |
242 | |
243 | |
244 PANTHER | |
245 | |
246 :: | |
247 | |
248 The PANTHER (Protein ANalysis THrough Evolutionary Relationships) | |
249 Classification System was designed to classify proteins (and their genes) | |
250 in order to facilitate high-throughput analysis. | |
251 hmmsearch from the HMM2.3.2 package (by Sean Eddy, | |
252 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). | |
253 and blastall from the Blast package (Altschul S.F. et al., 1997 [10]). | |
254 | |
255 | |
256 | |
257 **References** | |
258 | |
259 Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. | |
260 InterProScan: protein domains identifier (2005). | |
261 Nucleic Acids Res. 33 (Web Server issue) :W116-W120 | |
262 | |
263 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. | |
264 InterPro: the integrative protein signature database (2009). | |
265 Nucleic Acids Res. 37 (Database Issue) :D224-228 | |
266 | |
267 Galaxy Wrapper Author: | |
268 | |
269 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg | |
270 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter | |
271 | |
272 | |
273 | |
274 </help> | |
275 </tool> |