comparison interproscan.xml @ 4:fcedfe919603 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan commit 2f5d27a375fcc2e8d77914b3d9e402a9e2df2d97"

3:8ee90fc5fe11

<tool id="interproscan" name="Interproscan functional predictions of ORFs"  version="1.2">
    <description>Interproscan functional predictions of ORFs</description>
    <command>
## 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>&#38;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>&#38;1;
#end if

rm $tfile

    </command>
        <inputs>
            <param name="input" type="data" format="fasta" label="Protein Fasta File"/>

            <param name="appl" type="select" format="text" label="Applications to run" help="Select your programm.">
                <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option>
                <option value="seg">seg</option>
                <option value="signalp">signalp</option>
                <option value="tmhmm">tmhmm</option>
                <option value="fprintscan">fprintscan</option>
                <option value="patternscan">patternscan</option>
                <option value="profilescan">profilescan</option>
                <option value="superfamily">superfamily</option>
                <option value="hmmpir">hmmpir</option>
                <option value="hmmpfam">hmmpfam</option>
                <option value="hmmsmart">hmmsmart</option>
                <option value="hmmtigr">hmmtigr</option>
                <option value="hmmpanther">hmmpanther</option>
                <option value="hamap">hamap</option>
                <option value="gene3d">gene3d</option>
                <option value="coils">coils</option>
                <option value="blastprodom">blastprodom</option>
            </param>

            <param name="oformat" type="select" label="Output format" help="Please select a output format.">
                <option value="gff">gff</option>
                <option value="raw" selected="true">raw</option>
                <option value="txt">txt</option>
                <option value="html">html</option>
                <option value="xml">xml</option>
                <option value="ebixml">EBI header on top of xml</option>
            </param>

        </inputs>
    <outputs>

        <data format="txt" name="output" label="Interproscan calculation on ${on_string}">
            <change_format>
                <when input="oformat" value="html" format="html"/>
                <when input="oformat" value="xml" format="xml"/>
                <when input="oformat" value="ebixml" format="xml"/>
                <when input="oformat" value="gff" format="gff"/>
            </change_format>
        </data>

    </outputs>
    <requirements>
    </requirements>
    <help>
**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.

-----
Tools
-----

**PROSITE patterns**
 Some biologically significant amino acid patterns can be summarised in
 the form of regular expressions.
 ScanRegExp (by [e-mail]).

**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 [e-mail]).

**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,
 [e-mail], 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 [e-mail]
 and Yoann Beausse [e-mail])
 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,
 [e-mail], 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,
 [e-mail], 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,
 [e-mail], 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,
 [e-mail], 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,
 [e-mail], 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,
 [e-mail], http://hmmer.wustl.edu).
 and blastall from the Blast package (Altschul S.F. et al., 1997).

----------
References
----------

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

    </help>
</tool>

4:fcedfe919603

<tool id="interproscan" name="InterProScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
    <description>functional annotation</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">interproscan_4</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">interproscan</requirement>
    </requirements>
    <version_command>interproscan.sh --version</version_command>
    <command><![CDATA[
## Adapt properties file to use data from data table
mkdir -p \$HOME/.interproscan-5
&&
sed 's|^\(data.directory=\).*$|\1${database.fields.path}|' \$(dirname \$(readlink -f \$(command -v interproscan.sh)))/interproscan.properties > \$HOME/.interproscan-5/interproscan.properties
&&

## Now run interproscan
interproscan.sh

## disables the precalculated lookup service, all calculation will be run locally
-dp
--input '$input'
--seqtype $seqtype
-f ${','.join($oformat)}

#if $licensed.use == 'true' and $licensed.applications_licensed:
    --applications ${','.join($applications)},${','.join($licensed.applications_licensed)}
#else:
    --applications ${','.join($applications)}
#end if
--tempdir \$TEMP

$pathways
$goterms
$iprlookup

--cpu \${GALAXY_SLOTS:-4}

--output-file-base 'output'
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="fasta" label="Protein FASTA File"/>

        <param argument="--seqtype" type="select" label="Type of the input sequences" help="">
            <option value="p" selected="true">Protein</option>
            <option value="n">DNA / RNA</option>
        </param>

        <param name="database" label="InterProScan database" type="select">
            <options from_data_table="interproscan">
                <column name="value" index="0" />
                <column name="name" index="1" />
                <column name="path" index="3" />
                <filter type="sort_by" column="0" />
                <filter type="static_value" column="2" value="@TOOL_VERSION@" />
            </options>
        </param>

        <param name="applications" type="select" multiple="True" label="Applications to run" help="Select your program">
            <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on hidden Markov models (HMMs)</option>
            <option value="SFLD" selected="true">SFLD: a database of protein families based on hidden Markov models (HMMs)</option>
            <option value="SUPERFAMILY" selected="true">SUPERFAMILY: database of structural and functional annotation for all proteins and genomes</option>
            <option value="PANTHER" selected="true">PANTHER: Protein ANalysis THrough Evolutionary Relationships</option>
            <option value="Gene3D" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
            <option value="Hamap" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
            <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>
            <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
            <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
            <option value="CDD" selected="true">SMART: protein domains and families based on well-annotated multiple sequence alignment models</option>
            <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
            <option value="PIRSR" selected="true">PIRSR: protein families based on hidden Markov models (HMMs) and Site Rules</option>
            <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>
            <option value="Pfam" selected="true">Pfam: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
            <option value="MobiDBLite" selected="true">MobiDBLite: Prediction of intrinsically disordered regions in proteins</option>
            <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
        </param>

        <conditional name="licensed">
            <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" >
                <option value="false" selected="true">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false" />
            <when value="true">
                <param name="applications_licensed" type="select" multiple="True" label="Applications to run" help="Select your programm.">
                    <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide predictor</option>
                    <option value="SignalP_GRAM_NEGATIVE" selected="false">SignalP (gram-negative): signal peptide cleavage sites in amino acid sequences for gram-negative prokaryotes</option>
                    <option value="SignalP_EUK" selected="true">SignalP (eukaryotes): signal peptide cleavage sites in amino acid sequences for eukaryotes</option>
                    <option value="SignalP_GRAM_POSITIVE" selected="false">SignalP (Gram Positive Bacteria): signal peptide cleavage sites in amino acid sequences for gram-positive prokaryotes</option>
                    <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option>
                </param>
            </when>
        </conditional>

        <param argument="--pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean" label="Include pathway information"
            help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries."/>
        <param argument="--goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings"
            help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option."/>
        <param argument="--iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
            label="Provide additional mappings" help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into"/>

        <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/).">
            <option value="TSV" selected="true">Tab-separated values format (TSV)</option>
            <option value="GFF3">GFF3</option>
            <option value="XML">XML</option>
            <option value="JSON">JSON</option>
        </param>
    </inputs>

    <outputs>
        <data format="tabular" name="outfile_tsv" from_work_dir="output.tsv" label="InterProScan on ${on_string} (tsv)">
            <filter>oformat and 'TSV' in outputs</filter>
        </data>
        <data format="xml" name="outfile_xml" from_work_dir="output.xml" label="InterProScan on ${on_string} (xml)">
            <filter>oformat and 'XML' in outputs</filter>
        </data>
        <data format="gff3" name="outfile_gff3" from_work_dir="output.gff3" label="InterProScan on ${on_string} (gff3)">
            <filter>oformat and 'GFF3' in outputs</filter>
        </data>
        <data format="json" name="outfile_json" from_work_dir="output.json" label="InterProScan on ${on_string} (json)">
            <filter>oformat and 'JSON' in outputs</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input" value="prots.fa" />
            <param name="seqtype" value="p" />
            <param name="database" value="5.52-86.0" />
            <param name="applications" value="MobiDBLite" />
            <param name="oformat" value="TSV" />
            <output name="outfile_tsv">
                <assert_contents>
                    <has_text text="FUN_000011-T1" />
                    <has_text text="ea9924e11f7decc417e8d9ed8b9c682e" />
                    <has_text text="FUN_000012-T1" />
                    <has_text text="01beedc2fbf8012cba37f0c0d39aa071" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="prots.fa" />
            <param name="seqtype" value="p" />
            <param name="database" value="5.52-86.0" />
            <param name="applications" value="MobiDBLite" />
            <param name="oformat" value="TSV,GFF3,XML,JSON" />
            <output name="outfile_tsv">
                <assert_contents>
                    <has_text text="FUN_000011-T1" />
                    <has_text text="ea9924e11f7decc417e8d9ed8b9c682e" />
                    <has_text text="FUN_000012-T1" />
                    <has_text text="01beedc2fbf8012cba37f0c0d39aa071" />
                </assert_contents>
            </output>
            <output name="outfile_xml">
                <assert_contents>
                    <has_text text="mobidblite-location" />
                    <has_text text="Polyampholyte" />
                    <has_text text="consensus disorder prediction" />
                    <has_text text="FUN_000011-T1 FUN_000011" />
                </assert_contents>
            </output>
            <output name="outfile_gff3">
                <assert_contents>
                    <has_text text="protein_match" />
                    <has_text text="ID=FUN_000011-T1;md5=" />
                    <has_text text="MobiDBLite" />
                </assert_contents>
            </output>
            <output name="outfile_json">
                <assert_contents>
                    <has_text text="signatureLibraryRelease" />
                    <has_text text="disorder_prediction" />
                    <has_text text="Polyampholyte" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="transcripts.fa" />
            <param name="seqtype" value="n" />
            <param name="database" value="5.52-86.0" />
            <param name="applications" value="MobiDBLite" />
            <param name="oformat" value="TSV,GFF3,XML,JSON" />
            <output name="outfile_tsv">
                <assert_contents>
                    <has_text text="FUN_000018-T1_orf336" />
                    <has_text text="0b28fe115d4cc09260b038b19fb0b21d" />
                    <has_text text="FUN_000012-T1_orf133" />
                    <has_text text="01beedc2fbf8012cba37f0c0d39aa071" />
                </assert_contents>
            </output>
            <output name="outfile_xml">
                <assert_contents>
                    <has_text text="mobidblite-location" />
                    <has_text text="Polyampholyte" />
                    <has_text text="consensus disorder prediction" />
                    <has_text text="orf355" />
                </assert_contents>
            </output>
            <output name="outfile_gff3">
                <assert_contents>
                    <has_text text="protein_match" />
                    <has_text text="ID=FUN_000012-T1;" />
                    <has_text text="MobiDBLite" />
                </assert_contents>
            </output>
            <output name="outfile_json">
                <assert_contents>
                    <has_text text="signatureLibraryRelease" />
                    <has_text text="disorder_prediction" />
                    <has_text text="Polyampholyte" />
                </assert_contents>
            </output>
        </test>
        <test expect_failure="true">
            <param name="input" value="prots.fa" />
            <param name="seqtype" value="p" />
            <param name="database" value="5.52-86.0" />
            <param name="applications" value="MobiDBLite" />
            <conditional name="licensed">
                <param name="use" value="true" />
                <param name="applications_licensed" value="Phobius,TMHMM" />
            </conditional>
            <param name="oformat" value="TSV" />
            <assert_stdout>
                <!-- expected to be "deactivated" as they are not installed by default -->
                <has_text text="Analysis Phobius does not exist or is deactivated" />
                <has_text text="Analysis TMHMM does not exist or is deactivated" />
            </assert_stdout>
        </test>
    </tests>

    <help><![CDATA[

**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.

Phobius (licensed software), SignalP, SMART (licensed components) and TMHMM use
licensed code and data provided by third parties. If you wish to run these
analyses it will be necessary for you to obtain a licence from the vendor and
configure the Galaxy server InterProScan installation to use them.

**Input**

Required is a FASTA file containing protein or nucleotide sequences.

**Output**

In this version of InterProScan, you can retrieve output in any of the following five formats:

 * TSV: tab-separated values format
 * XML: XML format
 * GFF: The GFF 3.0 format
 * JSON: A JSON representation of the protein matches that can be visualised on https://www.ebi.ac.uk/interpro/result/InterProScan/

**Example Output**


::

  P51587  14086411a2cdf1c4cba63020e1622579        3418    Pfam    PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1        2670    2799    7.9E-43 T       15-03-2013
  P51587  14086411a2cdf1c4cba63020e1622579        3418    ProSiteProfiles PS50138 BRCA2 repeat profile.   1002    1036    0.0     T       18-03-2013      IPR002093       BRCA2 repeat    GO:0005515|GO:0006302
  P51587  14086411a2cdf1c4cba63020e1622579        3418    Gene3D  G3DSA:2.40.50.140               2966    3051    3.1E-52 T       15-03-2013
  ...


The TSV format presents the match data in columns as follows:

  - Protein Accession (e.g. P51587)
  - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
  - Sequence Length (e.g. 3418)
  - Analysis (e.g. Pfam / PRINTS / Gene3D)
  - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
  - Signature Description (e.g. BRCA2 repeat profile)
  - Start location
  - Stop location
  - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
  - Status - is the status of the match (T: true)
  - Date - is the date of the run
  - (InterProScan annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
  - (InterProScan annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
  - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
  - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)


**Extensible Markup Language (XML)**

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].

**Generic Feature Format Version 3 (GFF3)**

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].

**Example Output**


::

  ##gff-version 3
  ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
  ##sequence-region AACH01000027 1 1347
  ##seqid|source|type|start|end|score|strand|phase|attributes
  AACH01000027    provided_by_user        nucleic_acid    1       1347    .       +       .       Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
  AACH01000027    getorf  ORF     1       1347    .       +       .       Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
  AACH01000027    getorf  polypeptide     1       449     .       +       .       md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
  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"
  ##sequence-region 2
  ...
  >pep_AACH01000027_1_1347
  LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
  LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
  GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
  LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
  ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
  TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
  DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
  RSQKAKGVLIYRDDWISITPEIQLLFTEF
  ...
  >match$8_84_314
  KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
  RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
  LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
  AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS

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