InterProScan installation
-------------------------
1) Download the InterProScan software from ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan:
- RELEASE/latest/iprscan_v4.8.tar.gz - InterProScan itself
- BIN/4.x/iprscan_bin4.x_Linux64.tar.gz - Binaries for the various platforms
- DATA/latest_nopthr.tar.gz - databases used by InterProScan (except Panther)
- DATA/latest_pthr.tar.gz - panther database and indexes
- DATA/latest_match.tar.gz - match_complete.xml and interpro.xml files
InterProScan and the underlying applications are freely available under
the GNU licence agreement from the EBI's ftp server.
2) Install the InterProScan application as standalone on your Galaxy computer. Installation procedure:
- http://wiki.bioinformatics.ucdavis.edu/index.php/InterProScan
- ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/Installing_InterProScan.txt
3) Change the paths in the part of Galaxy wrapper "interproscan.xml" to the paths on your system
/home/katrien/iprscan/bin/iprscan
/home/katrien/iprscan/bin/converter.pl
4) Add the wrapper file "interproscan.xml" to Galaxy (reference: http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial).
- Make a directory "iprscan" under {GALAXY_ROOT_DIR}/tools and copy the wrapper file "interproscan.xml" to this directory.
- 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
Use a text editor to add a line for the interproscan.xml wrapper to e.g.the Sequence Annotation section.
- start up GALAXY again, open it in the web browser and test
InterProScan functionality
---------------------------
Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
These include SCOP, CATH, PFAM and SUPERFAMILY.
INPUT
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.
OUTPUT
Example for the raw format.
This is a basic tab delimited format useful for uploading the data into a relational database or concatenation of different runs.
is all on one line.
====== ================================================================ ======================================================================
column example description
====== ================================================================ ======================================================================
c1 NF00181542 the id of the input sequence.
c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique).
c3 272 the length of the sequence (in AA).
c4 HMMPIR the anaysis method launched.
c5 PIRSF001424 the database members entry for this match.
c6 Prephenate dehydratase the database member description for the entry.
c7 1 the start of the domain match.
c8 270 the end of the domain match.
c9 6.5e-141 the evalue of the match (reported by member database method).
c10 T the status of the match (T: true, ?: unknown).
c11 06-Aug-2005 the date of the run.
c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user).
c13 Prephenate dehydratase with ACT region the description of the InterPro entry.
c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry.
====== ================================================================ ======================================================================
Database updates
----------------
Typically these take place 2-3 times a year.
Tools
-----
PROSITE patterns
Some biologically significant amino acid patterns can be summarised in
the form of regular expressions.
ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk),
PROSITE profiles
There are a number of protein families as well as functional or
structural domains that cannot be detected using patterns due to their extreme
sequence divergence, so the use of techniques based on weight matrices
(also known as profiles) allows the detection of such proteins or domains.
A profile is a table of position-specific amino acid weights and gap costs.
The profile structure used in PROSITE is similar to but slightly more general
(Bucher P. et al., 1996 [7]) than the one introduced by M. Gribskov and
co-workers.
pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch).
PRINTS
The PRINTS database houses a collection of protein family fingerprints.
These are groups of motifs that together are diagnostically more
powerful than single motifs by making use of the biological context inherent in a
multiple-motif method. The fingerprinting method arose from the need for
a reliable technique for detecting members of large, highly divergent
protein super-families.
FingerPRINTScan (Scordis P. et al., 1999 [8]).
PFAM
Pfam is a database of protein domain families. Pfam contains curated
multiple sequence alignments for each family and corresponding hidden
Markov models (HMMs) (Eddy S.R., 1998 [9]).
Profile hidden Markov models are statistical models of the primary
structure consensus of a sequence family. The construction and use
of Pfam is tightly tied to the HMMER software package.
hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
PRODOM
ProDom is a database of protein domain families obtained by automated
analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
for analysing the domain arrangements of complex protein families and the
homology relationships in modular proteins. ProDom families are built by
an automated process based on a recursive use of PSI-BLAST homology
searches.
ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr
and Yoann Beausse beausse@toulouse.inra.fr)
a wrapper on top of the Blast package (Altschul S.F. et al., 1997 [10]).
SMART
SMART (a Simple Modular Architecture Research Tool) allows the
identification and annotation of genetically mobile domains and the
analysis of domain architectures. These domains are extensively
annotated with respect to phyletic distributions, functional class, tertiary
structures and functionally important residues. SMART alignments are
optimised manually and following construction of corresponding hidden Markov models (HMMs).
hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
TIGRFAMs
TIGRFAMs are a collection of protein families featuring curated multiple
sequence alignments, Hidden Markov Models (HMMs) and associated
information designed to support the automated functional identification
of proteins by sequence homology. Classification by equivalog family
(see below), where achievable, complements classification by orthologs,
superfamily, domain or motif. It provides the information best suited
for automatic assignment of specific functions to proteins from large
scale genome sequencing projects.
hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
PIR SuperFamily
PIR SuperFamily (PIRSF) is a classification system based on evolutionary
relationship of whole proteins.
hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
SUPERFAMILY
SUPERFAMILY is a library of profile hidden Markov models that represent
all proteins of known structure, based on SCOP.
hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
Optionally, predictions for coiled-coil, signal peptide cleavage sites
(SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
for details).
GENE3D
Gene3D is supplementary to the CATH database. This protein sequence database
contains proteins from complete genomes which have been clustered into protein
families and annotated with CATH domains, Pfam domains and functional
information from KEGG, GO, COG, Affymetrix and STRINGS.
hmmpfam from the HMM2.3.2 package (by Sean Eddy,
eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
PANTHER
The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
Classification System was designed to classify proteins (and their genes)
in order to facilitate high-throughput analysis.
hmmsearch from the HMM2.3.2 package (by Sean Eddy,
eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
and blastall from the Blast package (Altschul S.F. et al., 1997 [10]).
Author and affiliation
----------------------
Katrien Bernaerts and Domantas Motiejunas
corresponding author: gb-ctk-open-source-support@basf.com
12/07/2012
CropDesign N.V., a BASF Plant Science Company - Technologiepark 3, 9052 Zwijnaarde - Belgium
Terms of use
--------------------------
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.
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).
References
----------
Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R.
InterProScan: protein domains identifier (2005).
Nucleic Acids Res. 33 (Web Server issue) :W116-W120
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.
InterPro: the integrative protein signature database (2009).
Nucleic Acids Res. 37 (Database Issue) :D224-228
Previous Galaxy Wrapper Authors:
- Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
- Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis