OutputFormats

Matthew Fraser edited this page Sep 17, 2018 · 13 revisions

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 "IMPACT" XML format (XSD available here).
  • JSON: Full output of results in JSON format
  • GFF3: The GFF 3.0 format
  • HTML: An HTML representation of the protein matches
  • SVG: An Scalable Vector Graphics representation of the protein matches

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 HTML -i /path/to/sequences.fasta -b /path/to/output_file

or

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

These two equivalent commands will output the results in XML and HTML 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) - optional column; only displayed if -iprlookup option is switched on)
  13. (InterPro annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprlookup option is switched on)
  14. (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
  15. (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 here.

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>

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 JSON output format history.

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

Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)

InterProScan 5 outputs a single HTML/SVG file for each protein sequence analysed. The HTML/SVG file(s) are compressed into a single gzipped tar archive (or "tarball") that includes the resources (images, Javascript, style etc) to render the pages/images in a browser or image viewer. (Note that from version 5RC4, the SVG format has no external dependencies.)

The tarball will be named something similar to:

base_output_file_name.html.tar.gz OR base_output_file_name.svg.tar.gz

To access the HTML pages/SVG images, unzip the tarball using a command like:

tar -xvzf base_output_file_name.html(svg).tar.gz

You can then open the unzipped HTML/SVG files in any browser or image viewer (for SVG).

Example Output

SVG example output

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