Output formats
==============

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

-  `TSV <OutputFormats.html#tab-separated-values-format-tsv>`__: A simple tab-delimited file format
-  `XML <OutputFormats.html#extensible-markup-language-xml>`__: The InterProScan XML format (`XSD available
   here <OutputFormats.html#the-xml-schema-definition>`__).
-  `JSON <OutputFormats.html#javascript-object-notation-json>`__: Full output of results in JSON format
-  `GFF3 <OutputFormats.html#generic-feature-format-version-3-gff3>`__: The `GFF 3.0 <http://gmod.org/wiki/GFF#GFF3_Format>`__ format

InterProScan 5 can output results for protein and nucleotide sequences
in all formats. **Please note** you can only trace protein match
positions to the original nucleotide sequence with GFF3, XML and JSON
outputs.

You can override the default output formats using the **-f** option,
e.g.:

::

    ./interproscan.sh -f XML -f JSON -i /path/to/sequences.fasta -b /path/to/output_file

or

::

    ./interproscan.sh -f XML, JSON -i /path/to/sequences.fasta -b /path/to/output_file

These two equivalent commands will output the results in XML and JSON
format.

Tab-separated values format (TSV)
---------------------------------

Basic tab delimited format. Outputs only those sequences with domain
matches.

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:

1.  Protein accession (e.g. P51587)
2.  Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
3.  Sequence length (e.g. 3418)
4.  Analysis (e.g. Pfam / PRINTS / Gene3D)
5.  Signature accession (e.g. PF09103 / G3DSA:2.40.50.140)
6.  Signature description (e.g. BRCA2 repeat profile)
7.  Start location
8.  Stop location
9.  Score - is the e-value (or score) of the match reported by member
    database method (e.g. 3.1E-52)
10. Status - is the status of the match (T: true)
11. Date - is the date of the run
12. InterPro annotations - accession (e.g. IPR002093)
13. InterPro annotations - description (e.g. BRCA2 repeat)
14. GO annotations with their source(s), e.g. GO:0005515\(InterPro\)|GO:0006302\(PANTHER\)|GO:0007195\(InterPro,PANTHER\). This is an optional column; only displayed if the :code:`--goterms` option is switched on
15. Pathways annotations, e.g. REACT\_71. This is an optional column; only displayed if the :code:`--pathways` option is switched on

If a value is missing in a column, for example, the match has no InterPro annotation, a '-' is displayed.

Extensible Markup Language (XML)
--------------------------------

XML representation of the matches - this is the richest form of the
data. The XML Schema Definition (XSD) file links are below the example output.


Example output
~~~~~~~~~~~~~~

::

    <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
    <protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5" interproscan-version="5.26-65.0">
        <protein>
            <sequence md5="14086411a2cdf1c4cba63020e1622579">MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCPLLNSCLSESPVVLQCTHVTPQRDKSVVCGSLFHTPKFVKGRQTPKHISESLGAEVDPDMSWSSSLATPPTLSSTVLIVRNEEASETVFPHDTTANVKSYFSNHDESLKKNDRFIASVTDSENTNQREAASHGFGKTSGNSFKVNSCKDHIGKSMPNVLEDEVYETVVDTSEEDSFSLCFSKCRTKNLQKVRTSKTRKKIFHEANADECEKSKNQVKEKYSFVSEVEPNDTDPLDSNVAHQKPFESGSDKISKEVVPSLACEWSQLTLSGLNGAQMEKIPLLHISSCDQNISEKDLLDTENKRKKDFLTSENSLPRISSLPKSEKPLNEETVVNKRDEEQHLESHTDCILAVKQAISGTSPVASSFQGIKKSIFRIRESPKETFNASFSGHMTDPNFKKETEASESGLEIHTVCSQKEDSLCPNLIDNGSWPATTTQNSVALKNAGLISTLKKKTNKFIYAIHDETSYKGKKIPKDQKSELINCSAQFEANAFEAPLTFANADSGLLHSSVKRSCSQNDSEEPTLSLTSSFGTILRKCSRNETCSNNTVISQDLDYKEAKCNKEKLQLFITPEADSLSCLQEGQCENDPKSKKVSDIKEEVLAAACHPVQHSKVEYSDTDFQSQKSLLYDHENASTLILTPTSKDVLSNLVMISRGKESYKMSDKLKGNNYESDVELTKNIPMEKNQDVCALNENYKNVELLPPEKYMRVASPSRKVQFNQNTNLRVIQKNQEETTSISKITVNPDSEELFSDNENNFVFQVANERNNLALGNTKELHETDLTCVNEPIFKNSTMVLYGDTGDKQATQVSIKKDLVYVLAEENKNSVKQHIKMTLGQDLKSDISLNIDKIPEKNNDYMNKWAGLLGPISNHSFGGSFRTASNKEIKLSEHNIKKSKMFFKDIEEQYPTSLACVEIVNTLALDNQKKLSKPQSINTVSAHLQSSVVVSDCKNSHITPQMLFSKQDFNSNHNLTPSQKAEITELSTILEESGSQFEFTQFRKPSYILQKSTFEVPENQMTILKTTSEECRDADLHVIMNAPSIGQVDSSKQFEGTVEIKRKFAGLLKNDCNKSASGYLTDENEVGFRGFYSAHGTKLNVSTEALQKAVKLFSDIENISEETSAEVHPISLSSSKCHDSVVSMFKIENHNDKTVSEKNNKCQLILQNNIEMTTGTFVEEITENYKRNTENEDNKYTAASRNSHNLEFDGSDSSKNDTVCIHKDETDLLFTDQHNICLKLSGQFMKEGNTQIKEDLSDLTFLEVAKAQEACHGNTSNKEQLTATKTEQNIKDFETSDTFFQTASGKNISVAKESFNKIVNFFDQKPEELHNFSLNSELHSDIRKNKMDILSYEETDIVKHKILKESVPVGTGNQLVTFQGQPERDEKIKEPTLLGFHTASGKKVKIAKESLDKVKNLFDEKEQGTSEITSFSHQWAKTLKYREACKDLELACETIEITAAPKCKEMQNSLNNDKNLVSIETVVPPKLLSDNLCRQTENLKTSKSIFLKVKVHENVEKETAKSPATCYTNQSPYSVIENSALAFYTSCSRKTSVSQTSLLEAKKWLREGIFDGQPERINTADYVGNYLYENNSNSTIAENDKNHLSEKQDTYLSNSSMSNSYSYHSDEVYNDSGYLSKNKLDSGIEPVLKNVEDQKNTSFSKVISNVKDANAYPQTVNEDICVEELVTSSSPCKNKNAAIKLSISNSNNFEVGPPAFRIASGKIVCVSHETIKKVKDIFTDSFSKVIKENNENKSKICQTKIMAGCYEALDDSEDILHNSLDNDECSTHSHKVFADIQSEEILQHNQNMSGLEKVSKISPCDVSLETSDICKCSIGKLHKSVSSANTCGIFSTASGKSVQVSDASLQNARQVFSEIEDSTKQVFSKVLFKSNEHSDQLTREENTAIRTPEHLISQKGFSYNVVNSSAFSGFSTASGKQVSILESSLHKVKGVLEEFDLIRTEHSLHYSPTSRQNVSKILPRVDKRNPEHCVNSEMEKTCSKEFKLSNNLNVEGGSSENNHSIKVSPYLSQFQQDKQQLVLGTKVSLVENIHVLGKEQASPKNVKMEIGKTETFSDVPVKTNIEVCSTYSKDSENYFETEAVEIAKAFMEDDELTDSKLPSHATHSLFTCPENEEMVLSNSRIGKRRGEPLILVGEPSIKRNLLNEFDRIIENQEKSLKASKSTPDGTIKDRRLFMHHVSLEPITCVPFRTTKERQEIQNPNFTAPGQEFLSKSHLYEHLTLEKSSSNLAVSGHPFYQVSATRNEKMRHLITTGRPTKVFVPPFKTKSHFHRVEQCVRNINLEENRQKQNIDGHGSDDSKNKINDNEIHQFNKNNSNQAAAVTFTKCEEEPLDLITSLQNARDIQDMRIKKKQRQRVFPQPGSLYLAKTSTLPRISLKAAVGGQVPSACSHKQLYTYGVSKHCIKINSKNAESFQFHTEDYFGKESLWTGKGIQLADGGWLIPSNDGKAGKEEFYRALCDTPGVDPKLISRIWVYNHYRWIIWKLAAMECAFPKEFANRCLSPERVLLQLKYRYDTEIDRSRRSAIKKIMERDDTAAKTLVLCVSDIISLSANISETSSNKTSSADTQKVAIIELTDGWYAVKAQLDPPLLAVLKNGRLTVGQKIILHGAELVGSPDACTPLEAPESLMLKISANSTRPARWYTKLGFFPDPRPFPLPLSSLFSDGGNVGCVDVIIQRAYPIQWMEKTSSGLYIFRNEREEEKEAAKYVEAQQKRLEALFTKIQEEFEEHEENTTKPYLPSRALTRQQVRALQDGAELYEAVKNAADPAYLEGYFSEEQLRALNNHRQMLNDKKQAQIQLEIRKAMESAEQKEQGLSRDVTTVWKLRIVSYSKKEKDSVILSIWRPSSDLYSLLTEGKRYRIYHLATSKSKSKSERANIQLAATKKTQYQQLPVSDEILFQIYQPREPLHFSKFLDPDFQPSCSEVDLIGFVVSVVKKTGLAPFVYLSDECYNLLAIKFWIDLNEDIIKPHMLIAASNLQWRPESKSGLLTLFAGDFSVFSASPKEGHFQETFNKMKNTVENIDILCNEAENKLMHILHANDPKWSTPTKDCTSGPYTAQIIPGTGNKLLMSSPNCEIYYQSPLSLCMAKRKSVSTPVSAQMTSKSCKGEKEIDDQKNCKKRRALDFLSRLPLPPPVSPICTFVSPAAQKAFQPPRSCGTKYETPIKKKELNSPQMTPFKKFNEISLLESNSIADEELALINTQALLSGSTGEKQFISVSESTRTAPTSSEDYLRLKRRCTTSLIKEQESSQASTEECEKNKQDTITTKKYI</sequence>
            <xref id="P51587"/>
            <matches>
    ...
                <hmmer3-match score="341.9" evalue="0.0">
                    <signature name="BRCA-2_helical" desc="BRCA2, helical" ac="PF09169">
                        <entry type="DOMAIN" name="BRCA2_hlx" desc="Breast cancer type 2 susceptibility protein, helical domain" ac="IPR015252">
                            <go-xref category="BIOLOGICAL_PROCESS" name="double-strand break repair via homologous recombination" id="GO:0000724" db="GO"/>
                            <go-xref category="MOLECULAR_FUNCTION" name="single-stranded DNA binding" id="GO:0003697" db="GO"/>
                            <go-xref category="BIOLOGICAL_PROCESS" name="DNA recombination" id="GO:0006310" db="GO"/>
                        </entry>
                        <models>
                            <model name="BRCA-2_helical" desc="BRCA2, helical" ac="PF09169"/>
                        </models>
                        <signature-library-release version="27.0" library="PFAM"/>
                    </signature>
                    <locations>
                        <hmmer3-location env-start="2479" env-end="2667" hmm-end="195" hmm-start="1" evalue="9.6E-102" score="0.0" end="2667" start="2479"/>
                    </locations>
                </hmmer3-match>
    ...
                <superfamilyhmmer3-match evalue="0.0">
                    <signature name="BRCA2 helical domain" ac="SSF81872">
                        <entry type="DOMAIN" name="BRCA2_hlx" desc="Breast cancer type 2 susceptibility protein, helical domain" ac="IPR015252">
                            <go-xref category="BIOLOGICAL_PROCESS" name="double-strand break repair via homologous recombination" id="GO:0000724" db="GO"/>
                            <go-xref category="MOLECULAR_FUNCTION" name="single-stranded DNA binding" id="GO:0003697" db="GO"/>
                            <go-xref category="BIOLOGICAL_PROCESS" name="DNA recombination" id="GO:0006310" db="GO"/>
                        </entry>
                        <models>
                            <model name="BRCA2 helical domain" ac="0039279"/>
                            <model name="BRCA2 helical domain" ac="0040951"/>
                        </models>
                        <signature-library-release version="1.75" library="SUPERFAMILY"/>
                    </signature>
                    <locations>
                        <superfamilyhmmer3-location end="2668" start="2479"/>
                    </locations>
                </superfamilyhmmer3-match>
    ...
                <rpsblast-match>
                    <signature ac="cd08964" desc="L-asparaginase_II" name="L-asparaginase_II">
                        <models>
                            <model ac="cd08964" desc="L-asparaginase_II" name="L-asparaginase_II"/>
                        </models>
                        <signature-library-release library="CDD" version="3.14"/>
                    </signature>
                    <locations>
                        <rpsblast-location evalue="8.66035E-152" score="433.09" start="50" end="364">
                            <sites>
                                <rpsblast-site description="homotetramer interface" numLocations="51">
    <site-locations>
        <site-location residue="Y" start="271" end="271"/>
        <site-location residue="R" start="246" end="246"/>
        <site-location residue="Y" start="229" end="229"/>
        ...
    </site-locations>
                                </rpsblast-site>
                                ...
                            </sites>
                        </rpsblast-location>
                    </locations>
                </rpsblast-match>
                ...
            </matches>
        </protein>
    </protein-matches>

The XML Schema Definition
-------------------------
The XML Schema Definition (XSD) is available
`here <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/>`__.


Listed below are the XSD files for the InterProScan 5 XML output format (with the InterProScan release versions they apply to noted in brackets afterwards).

- `interproscan-model-4.6.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-4.6.xsd>`__ (as produced by InterProScan 5 from version 5.63-95.0 onwards)
- `interproscan-model-4.5.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-4.5.xsd>`__ (as produced by InterProScan 5 from version 5.51-85.0 to 5.62-94.0)
- `interproscan-model-3.0.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-3.0.xsd>`__ (as produced by InterProScan 5 from version 5.31-70.0 to 5.50-84.0)
- `interproscan-model-2.2.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-2.2.xsd>`__ (as produced by InterProScan 5 from version 5.28-67.0 to 5.30-69.0)
- `interproscan-model-2.1.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-2.1.xsd>`__ (as produced by InterProScan 5 from version 5.26-65.0 to 5.27-66.0)
- `interproscan-model-2.0.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-2.0.xsd>`__ (as produced by InterProScan 5 from version 5.21-60.0 to 5.25-64.0)
- `interproscan-model-1.4.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-1.4.xsd>`__ (as produced by InterProScan 5 in version 5.20-59.0 only)
- `interproscan-model-1.3.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-1.3.xsd>`__ (as produced by InterProScan 5 in version 5.19-58.0 only)
- `interproscan-model-1.2.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-1.2.xsd>`__ (as produced by InterProScan 5 from version 5.17-56.0 to 5.18-57.0)
- `interproscan-model-1.1.xsd <htpp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-1.1.xsd>`__ (as produced by InterProScan 5 from version RC7 to 5.16-55.0)
- `interproscan-model-1.0.xsd <http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas/interproscan-model-1.0.xsd>`__ (InterProScan 5 version RC1 to RC6)


JavaScript Object Notation (JSON)
---------------------------------

JSON representation of the matches - an alternative to XML format. As
new releases are made public, the changes to the expected JSON format
are documented in :ref:`Change log for InterProScan JSON output format`.

Example output
~~~~~~~~~~~~~~

::

    {
     "interproscan-version": "5.26-65.0",
    "results": [{
      "sequence" : "MSKIGKSIRLERIIDRKTRKTVIVPMDHGLTVGPIPGLIDLAAAVDKVAEGGANAVLGHMGLPLYGHRGYGKDVGLIIHLSASTSLGPDANHKVLVTRVEDAIRVGADGVSIHVNVGAEDEAEMLRDLGMVARRCDLWGMPLLAMMYPRGAKVRSEHSVEYVKHAARVGAELGVDIVKTNYTGSPETFREVVRGCPAPVVIAGGPKMDTEADLLQMVYDAMQAGAAGISIGRNIFQAENPTLLTRKLSKIVHEGYTPEEAARLKL",
      "md5" : "88d47cc807fe8e977130b0cc93e0bd61",
      "matches" : [ {
        "signature" : {
          "accession" : "PIRSF038992",
          "name" : "Aldolase_Ia",
          "description" : null,
          "type" : null,
          "signatureLibraryRelease" : {
            "library" : "PIRSF",
            "version" : "3.01"
          },
          "models" : {
            "PIRSF038992" : {
              "accession" : "PIRSF038992",
              "name" : "Aldolase_Ia",
              "description" : null,
              "key" : "PIRSF038992"
            }
          },
          "entry" : {
            "accession" : "IPR002915",
            "name" : "DeoC/FbaB/lacD_aldolase",
            "description" : "DeoC/FbaB/ lacD aldolase",
            "type" : "FAMILY",
            "goXRefs" : [ {
              "identifier" : "GO:0016829",
              "name" : "lyase activity",
              "databaseName" : "GO",
              "category" : "MOLECULAR_FUNCTION"
            } ],
            "pathwayXRefs" : [ {
              "identifier" : "R-HSA-71336",
              "name" : "Pentose phosphate pathway (hexose monophosphate shunt)",
              "databaseName" : "Reactome"
            }, {
              "identifier" : "R-HSA-6798695",
              "name" : "Neutrophil degranulation",
              "databaseName" : "Reactome"
            } ]
          }
        },
        "locations" : [ {
          "start" : 1,
          "end" : 265,
          "hmmStart" : 2,
          "hmmEnd" : 262,
          "hmmBounds" : "INCOMPLETE",
          "evalue" : 3.3E-94,
          "score" : 302.6,
          "envelopeStart" : 1,
          "envelopeEnd" : 265
        } ],
        "evalue" : 3.0E-94,
        "score" : 302.7
      }, {
        ...
    }]
    }

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 http://www.sequenceontology.org/gff3.shtml.

**Please note** in GFF3 sequence identifiers "...may contain any
characters, but must escape any characters not in the set..." (1)

::

    a-zA-Z0-9.:^*$@!+_?-|.

1. http://www.sequenceontology.org/gff3.shtml

Example output
~~~~~~~~~~~~~~

::

    ##gff-version 3
    ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
    ##interproscan-version 5.26-65.0
    ##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