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1 InterProScan installation
2 -------------------------
3
4 1) Download the InterProScan software from ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan:
5
6 - RELEASE/latest/iprscan_v4.8.tar.gz - InterProScan itself
7 - BIN/4.x/iprscan_bin4.x_Linux64.tar.gz - Binaries for the various platforms
8 - DATA/latest_nopthr.tar.gz - databases used by InterProScan (except Panther)
9 - DATA/latest_pthr.tar.gz - panther database and indexes
10 - DATA/latest_match.tar.gz - match_complete.xml and interpro.xml files
11
12 InterProScan and the underlying applications are freely available under
13 the GNU licence agreement from the EBI's ftp server.
14
15 2) Install the InterProScan application as standalone on your Galaxy computer. Installation procedure:
16
17 - http://wiki.bioinformatics.ucdavis.edu/index.php/InterProScan
18 - ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/Installing_InterProScan.txt
19
20 3) Change the paths in the <command> part of Galaxy wrapper "interproscan.xml" to the paths on your system
21
22 /home/katrien/iprscan/bin/iprscan
23 /home/katrien/iprscan/bin/converter.pl
24
25 4) Add the wrapper file "interproscan.xml" to Galaxy (reference: http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial).
26
27 - Make a directory "iprscan" under {GALAXY_ROOT_DIR}/tools and copy the wrapper file "interproscan.xml" to this directory.
28 - Make GALAXY aware of the new tool: GALAXY knows about installed tools (and also what to display on the left pane) from the file {GALAXY_ROOT_DIR}/tool_conf.xml
29 Use a text editor to add a line for the interproscan.xml wrapper to e.g.the Sequence Annotation section.
30
31 <label text="My Tools" id="My tools" />
32 <section name="Sequence Annotation" id="sequence_annotation" >
33 <tool file="iprscan/interproscan.xml" />
34 </section>
35
36 - start up GALAXY again, open it in the web browser and test
37
38
39 InterProScan functionality
40 ---------------------------
41
42 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
43 These include SCOP, CATH, PFAM and SUPERFAMILY.
44
45 INPUT
46
47 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.
48
49 OUTPUT
50
51 Example for the raw format.
52 This is a basic tab delimited format useful for uploading the data into a relational database or concatenation of different runs.
53 is all on one line.
54
55 ====== ================================================================ ======================================================================
56 column example description
57 ====== ================================================================ ======================================================================
58 c1 NF00181542 the id of the input sequence.
59 c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique).
60 c3 272 the length of the sequence (in AA).
61 c4 HMMPIR the anaysis method launched.
62 c5 PIRSF001424 the database members entry for this match.
63 c6 Prephenate dehydratase the database member description for the entry.
64 c7 1 the start of the domain match.
65 c8 270 the end of the domain match.
66 c9 6.5e-141 the evalue of the match (reported by member database method).
67 c10 T the status of the match (T: true, ?: unknown).
68 c11 06-Aug-2005 the date of the run.
69 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user).
70 c13 Prephenate dehydratase with ACT region the description of the InterPro entry.
71 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry.
72 ====== ================================================================ ======================================================================
73
74
75 Database updates
76 ----------------
77
78 Typically these take place 2-3 times a year.
79
80
81 Tools
82 -----
83
84 PROSITE patterns
85 Some biologically significant amino acid patterns can be summarised in
86 the form of regular expressions.
87 ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk),
88
89 PROSITE profiles
90 There are a number of protein families as well as functional or
91 structural domains that cannot be detected using patterns due to their extreme
92 sequence divergence, so the use of techniques based on weight matrices
93 (also known as profiles) allows the detection of such proteins or domains.
94 A profile is a table of position-specific amino acid weights and gap costs.
95 The profile structure used in PROSITE is similar to but slightly more general
96 (Bucher P. et al., 1996 [7]) than the one introduced by M. Gribskov and
97 co-workers.
98 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch).
99
100 PRINTS
101 The PRINTS database houses a collection of protein family fingerprints.
102 These are groups of motifs that together are diagnostically more
103 powerful than single motifs by making use of the biological context inherent in a
104 multiple-motif method. The fingerprinting method arose from the need for
105 a reliable technique for detecting members of large, highly divergent
106 protein super-families.
107 FingerPRINTScan (Scordis P. et al., 1999 [8]).
108
109 PFAM
110 Pfam is a database of protein domain families. Pfam contains curated
111 multiple sequence alignments for each family and corresponding hidden
112 Markov models (HMMs) (Eddy S.R., 1998 [9]).
113 Profile hidden Markov models are statistical models of the primary
114 structure consensus of a sequence family. The construction and use
115 of Pfam is tightly tied to the HMMER software package.
116 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
117 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
118
119 PRODOM
120 ProDom is a database of protein domain families obtained by automated
121 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
122 for analysing the domain arrangements of complex protein families and the
123 homology relationships in modular proteins. ProDom families are built by
124 an automated process based on a recursive use of PSI-BLAST homology
125 searches.
126 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr
127 and Yoann Beausse beausse@toulouse.inra.fr)
128 a wrapper on top of the Blast package (Altschul S.F. et al., 1997 [10]).
129
130
131 SMART
132 SMART (a Simple Modular Architecture Research Tool) allows the
133 identification and annotation of genetically mobile domains and the
134 analysis of domain architectures. These domains are extensively
135 annotated with respect to phyletic distributions, functional class, tertiary
136 structures and functionally important residues. SMART alignments are
137 optimised manually and following construction of corresponding hidden Markov models (HMMs).
138 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
139 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
140
141
142 TIGRFAMs
143 TIGRFAMs are a collection of protein families featuring curated multiple
144 sequence alignments, Hidden Markov Models (HMMs) and associated
145 information designed to support the automated functional identification
146 of proteins by sequence homology. Classification by equivalog family
147 (see below), where achievable, complements classification by orthologs,
148 superfamily, domain or motif. It provides the information best suited
149 for automatic assignment of specific functions to proteins from large
150 scale genome sequencing projects.
151 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
152 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
153
154 PIR SuperFamily
155 PIR SuperFamily (PIRSF) is a classification system based on evolutionary
156 relationship of whole proteins.
157 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
158 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
159
160 SUPERFAMILY
161 SUPERFAMILY is a library of profile hidden Markov models that represent
162 all proteins of known structure, based on SCOP.
163 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
164 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
165 Optionally, predictions for coiled-coil, signal peptide cleavage sites
166 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
167 for details).
168
169
170 GENE3D
171 Gene3D is supplementary to the CATH database. This protein sequence database
172 contains proteins from complete genomes which have been clustered into protein
173 families and annotated with CATH domains, Pfam domains and functional
174 information from KEGG, GO, COG, Affymetrix and STRINGS.
175 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
176 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
177
178
179 PANTHER
180 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
181 Classification System was designed to classify proteins (and their genes)
182 in order to facilitate high-throughput analysis.
183 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
184 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
185 and blastall from the Blast package (Altschul S.F. et al., 1997 [10]).
186
187
188 Author and affiliation
189 ----------------------
190
191 Katrien Bernaerts and Domantas Motiejunas
192 corresponding author: gb-ctk-open-source-support@basf.com
193 12/07/2012
194
195 CropDesign N.V., a BASF Plant Science Company - Technologiepark 3, 9052 Zwijnaarde - Belgium
196
197
198 Terms of use
199 --------------------------
200 Galaxy wrapper for InterProScan – sequence annotation tool - Copyright (C) 2012 CropDesign N.V. - this software may be used, copied and redistributed, with or without modification freely, without advance permission, provided that the above Copyright statement is reproduced with each copy.
201 THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE (INCLUDING NEGLIGENCE OR OTHERWISE).
202
203
204 References
205 ----------
206
207 Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R.
208 InterProScan: protein domains identifier (2005).
209 Nucleic Acids Res. 33 (Web Server issue) :W116-W120
210
211 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.
212 InterPro: the integrative protein signature database (2009).
213 Nucleic Acids Res. 37 (Database Issue) :D224-228
214
215 Previous Galaxy Wrapper Authors:
216 - Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
217 - Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
218