[maker-devel] databases supported with ipr_update_gff script

[Carson Holt]

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/ <https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/>, Uniprot —> https://www.uniprot.org/docs/dbxref <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 <vsoza at uw.edu> 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/
> 
> 
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