[maker-devel] 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/