Re: [Gmod-ajax] [apollo] InterProScan loading into JBrowse

[Colin <col...@gm...>]

It looks like maybe these annotations are in protein space. I guess what
you are looking for is to convert this protein annotation into genome
coordinates.

This isn't something that is done by jbrowse tools.

I would maybe ask the BRAKER team, as they probably work with this type of
scenario often.

-Colin

On Tue, Jul 23, 2019 at 12:52 PM Lbl <nat...@lb...> wrote:

> Cross posting to jbrowse list
>
> On Jul 23, 2019, at 12:17 AM, Michał T. Lorenc <m.t...@gm...>
> wrote:
>
> Hi
> Our annotation is based on BRAKER2 additionally I ran InterProScan and I
> got GFF3, TSV and XML. I tried to load the GFF3 file using
>
>
> *> perl /apollo/jbrowse/bin/flatfile-to-json.pl
> <http://flatfile-to-json.pl> --gff
> /apollo/braker-soft_utr-interproscan.gff3 --compress --trackType
> HTMLFeatures --trackLabel "interproscan" --out /apollo/*
>
> It appears that no InterProScan results has been loaded. I assume that the
> InterProScan's GFF3 file does not contain any chromosome names:
>
>
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> *##gff-version 3##feature-ontology
> http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
> <http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269>##interproscan-version
> 5.36-75.0##sequence-region g109343.t1 1 1358g109343.t1      .
> polypeptide     1       1358    .       +       .
> ID=g109343.t1;md5=3e908dc966fefe367e64dc9d98b0d3abg109343.t1
> ProSiteProfiles protein_match   628     724     18.261  +       .
> date=20-07-2019;Target=g109343.t1 628
> 724;Ontology_term="GO:0015074";ID=match$1_628_724;signature_desc=Integrase
> catalytic domain
> profile.;Name=PS50994;status=T;Dbxref="InterPro:IPR001584"g109343.t1
> SUPERFAMILY     protein_match   586     624     4.19E-5 +       .
> date=20-07-2019;Target=g109343.t1 586
> 624;Ontology_term="GO:0003676","GO:0008270";ID=match$2_586_624;Name=SSF57756;status=T;Dbxref="InterPro:IPR036875"g109343.t1
> SUPERFAMILY     protein_match   622     725     4.93E-29        +
> .       date=20-07-2019;Target=g109343.t1 622
> 725;ID=match$3_622_725;Name=SSF53098;status=T;Dbxref="InterPro:IPR012337"g109343.t1
> ProSiteProfiles protein_match   278     294     9.636   +       .
> date=20-07-2019;Target=g109343.t1 278
> 294;Ontology_term="GO:0003676","GO:0008270";ID=match$4_278_294;signature_desc=Zinc
> finger CCHC-type
> profile.;Name=PS50158;status=T;Dbxref="InterPro:IPR001878"g109343.t1
> SMART   protein_match   600     616     0.36    +       .
> date=20-07-2019;Target=g109343.t1 600
> 616;Ontology_term="GO:0003676","GO:0008270";ID=match$5_600_616;Name=SM00343;status=T;Dbxref="InterPro:IPR001878"g109343.t1
> SMART   protein_match   278     294     6.3E-4  +       .
> date=20-07-2019;Target=g109343.t1 278
> 294;Ontology_term="GO:0003676","GO:0008270";ID=match$5_278_294;Name=SM00343;status=T;Dbxref="InterPro:IPR001878"g109343.t1
> Pfam    protein_match   82      216     1.2E-24 +       .
> date=20-07-2019;Target=g109343.t1 82
> 216;ID=match$6_82_216;signature_desc=gag-polypeptide of LTR
> copia-type;Name=PF14223;status=T*
>
> Is there a solution how to load InterProScan results as a track into
> JBrowse or are there any scripts which combine InterProScan with BRAKER2?
>
> Thank you in advance,
>
> Michal
>
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