Output formats¶

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

TSV: A simple tab-delimited file format
XML: The InterProScan XML format (XSD available here).
JSON: Full output of results in JSON format
GFF3: The GFF 3.0 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:

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 (or score) 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
InterPro annotations - accession (e.g. IPR002093)
InterPro annotations - description (e.g. BRCA2 repeat)
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 --goterms option is switched on
Pathways annotations, e.g. REACT_71. This is an optional column; only displayed if the --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.

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 (as produced by InterProScan 5 from version 5.63-95.0 onwards)
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 (as produced by InterProScan 5 from version 5.31-70.0 to 5.50-84.0)
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 (as produced by InterProScan 5 from version 5.26-65.0 to 5.27-66.0)
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 (as produced by InterProScan 5 in version 5.20-59.0 only)
interproscan-model-1.3.xsd (as produced by InterProScan 5 in version 5.19-58.0 only)
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 (as produced by InterProScan 5 from version RC7 to 5.16-55.0)
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 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.:^*$@!+_?-|.

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