databases supported with ipr_update_gff script

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databases supported with ipr_update_gff script

Valerie Soza
Hi Maker community

I am using the accessory scripts provided with Maker 2.3.19 to do some functional annotations of genes predicted with the Maker pipeline. For integrating information from InterProScan, I want to use the ipr_update_gff script. When I looked at the script, I found the following lines:

my %db_map = (BlastProDom  => 'ProDom',
                  FPrintScan   => 'PRINTS',
                  Gene3D       => 'Gene3D',
                  HMMPanther   => 'PANTHER',
                  HMMPfam      => 'Pfam',
                  HMMPIR       => 'PIR',
                  HMMSmart     => 'SMART',
                  HMMTigr      => 'JCVI_TIGRFAMS',
                  PatternScan  => 'Prosite',
                  ProfileScan  => 'Prosite',
                  );

Does this indicate that these are the only databases that the script will extract information for from an InterProScan report?

I wanted to use all databases currently available from InterProScan 5, InterProScan version 5.28-67.0, see below, but am wondering whether the Maker script will recognize results from all of the following databases?

        • CDD
        • COILS
        • Gene3D
        • HAMAP
        • MOBIDB
        • PANTHER
        • Pfam
        • PIRSF
        • PRINTS
        • ProDom
        • PROSITE (Profiles and Patterns)
        • SFLD
        • SMART (unlicensed components only by default - this analysis has simplified post-processing that includes an E-value filter, however you should not expect it to give the same match output as the fully licensed version of SMART)
        • SUPERFAMILY
        • TIGRFAMs

Thanks.

-Valerie

Valerie Soza, Ph.D.
c/o Hall Lab
Department of Biology
University of Washington
Johnson Hall 202A
Box 351800
Seattle, WA 98195-1800
206-543-6740
http://staff.washington.edu/vsoza/


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Re: databases supported with ipr_update_gff script

Carson Holt-2
Those are just for name conversion (takes what in the report and rename it to a known DB_xref term). If there is no conversion, the name will stay the same as in the report (unaltered). Different databases have there own db_xref values. I can’t remember where the ones we are using came from (I think it was from GMOD’s Chado database). NCBI also has their own —> https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/, Uniprot —> https://www.uniprot.org/docs/dbxref, and you can search around for others as well.

—Carson


On May 24, 2018, at 5:19 PM, Valerie Soza <[hidden email]> wrote:

Hi Maker community

I am using the accessory scripts provided with Maker 2.3.19 to do some functional annotations of genes predicted with the Maker pipeline. For integrating information from InterProScan, I want to use the ipr_update_gff script. When I looked at the script, I found the following lines:

my %db_map = (BlastProDom  => 'ProDom',
 FPrintScan   => 'PRINTS',
 Gene3D       => 'Gene3D',
 HMMPanther   => 'PANTHER',
 HMMPfam      => 'Pfam',
 HMMPIR       => 'PIR',
 HMMSmart     => 'SMART',
 HMMTigr      => 'JCVI_TIGRFAMS',
 PatternScan  => 'Prosite',
 ProfileScan  => 'Prosite',
 );

Does this indicate that these are the only databases that the script will extract information for from an InterProScan report?

I wanted to use all databases currently available from InterProScan 5, InterProScan version 5.28-67.0, see below, but am wondering whether the Maker script will recognize results from all of the following databases?

• CDD
• COILS
• Gene3D
• HAMAP
• MOBIDB
• PANTHER
• Pfam
• PIRSF
• PRINTS
• ProDom
• PROSITE (Profiles and Patterns)
• SFLD
• SMART (unlicensed components only by default - this analysis has simplified post-processing that includes an E-value filter, however you should not expect it to give the same match output as the fully licensed version of SMART)
• SUPERFAMILY
• TIGRFAMs

Thanks.

-Valerie

Valerie Soza, Ph.D.
c/o Hall Lab
Department of Biology
University of Washington
Johnson Hall 202A
Box 351800
Seattle, WA 98195-1800
206-543-6740
http://staff.washington.edu/vsoza/


_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org