[maker-devel] clarification on creating a standard build

[Valerie Soza]

Hi MAKER community

I am trying to create a standard build as indicated in the Campbell et al. 2014 papers in Plant Physiology and Current Protocols in Bioinformatics. I was following the protocol as outlined in Current Protocols in Bioinformatics, but then came across this thread in the MAKER google forum: https://groups.google.com/forum/#!searchin/maker-devel/quality_filter%7Csort:date/maker-devel/97aNJkT3bgk/mpL7V5QWAAAJ.

I can’t reply to this original thread, but I am trying to follow Carson’s suggestion for a standard build using this protocol instead now:
"One note I’d like to make, is that doing a second round with keep_preds=1 is the wrong procedure (only do that if you really want to keep everything - i.e. in some fungi or oomycetes). Rather you should use InterProScan to evaluate the rejected models in the non-overlapping.abinit.proteins.fasta file, then grep the ones that have an IPR domain out of the GFF3 (will be match/match_part features) and then pass them to pred_gff in a separate run (just updates the format to gene/mRNA/exon/CDSwith proper reading frame). You can then merge the resulting GFF3's and fasta files.”

Instead of doing a second round of annotations with keep_preds=1, I am using my original annotations with keep_preds=0. I have used InterProScan on the non-overlapping.abinit.proteins.fasta. I am unclear as to what gff3 file to use to grep for genes with IPR domains from the non-overlapping.abinit.proteins.fasta file. Genes from the non-overlapping.abinit.proteins.fasta file are not in my .all.gff file created by the gff3_merge script. 

What gff3 file should I be using to resurrect proteins with IPR domains from the non-overlapping.abinit.proteins.fasta? Should I be doing an annotation with keep_preds=1 as well, and resurrecting genes with IPR domains from this gff3?

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/