Interproscan functional predictions of ORFs
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
## create temp directory
#import tempfile, os
#set $tfile = tempfile.mkstemp()[1]
sed 's/ /_/g' $input > $tfile;
## Hack, because interproscan does not seem to produce gff output even if it is configured
#if str($oformat) == "gff":
#set $tfile2 = tempfile.mkstemp()[1]
iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl 2>&1;
converter.pl -format gff3 -input $tfile2 -output $output;
rm $tfile2;
#else
iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl 2>&1;
#end if
rm $tfile
**What it does**
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**
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.
**Output**
Example for the raw format.
The output will consist of a tabular file with 14 columns and can be easily concatenated or filtered.
====== ================================================================ ======================================================================
column example description
====== ================================================================ ======================================================================
c1 NF00181542 id of the input sequence
c2 27A9BBAC0587AB84 crc64 (checksum) of the protein sequence (supposed to be unique)
c3 272 length of the sequence (in AA)
c4 HMMPIR anaysis method launched.
c5 PIRSF001424 database members entry for this match
c6 Prephenate dehydratase database member description for the entry
c7 1 start of the domain match
c8 270 end of the domain match
c9 6.5e-141 evalue of the match (reported by member database method)
c10 T status of the match (T: true, ?: unknown)
c11 06-Aug-2005 date of the run.
c12 IPR008237 corresponding InterPro entry (if iprlookup requested by the user)
c13 Prephenate dehydratase with ACT region description of the InterPro entry
c14 Molecular Function:prephenate dehydratase activity (GO:0004664) GO (gene ontology) description for the InterPro entry
====== ================================================================ ======================================================================
**Database updates**
Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases.
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Tools
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**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) 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).
**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).
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).
**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).
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References
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Zdobnov EM, Apweiler R (2001)
InterProScan an integration platform for the signature-recognition methods in InterPro.
Bioinformatics 17, 847-848.
http://dx.doi.org/10.1093/bioinformatics/17.9.847
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
InterProScan: protein domains identifier.
Nucleic Acids Research 33 (Web Server issue), W116-W120.
http://dx.doi.org/10.1093/nar/gki442
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)
InterPro: the integrative protein signature database.
Nucleic Acids Research 37 (Database Issue), D224-228.
http://dx.doi.org/10.1093/nar/gkn785
This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan
**Galaxy Wrapper Author**::
* Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
* Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter