[maker-devel] associating gene names between related strains

[Carson Holt]

maker_map_ids does a translation (i.e. change gene-A to smug1), so you need
to know which genes you want to translate names to (two column input file,
column 1 -> original ID, column 2 -> new ID).  I’m not sure EST forward is
the best way to do this, although I do think maker_map_ids is the tool to
use in the end.  The question is how to make a list of IDs to translate as
the input to maker_map_ids?

I would actually just use BLASTP against the reference strain, and then do
reciprocal best BLAST hits.  To do this you BLAST your reference proteins
against your maker proteins.  Then do the opposite, BLAST your  maker
proteins against your reference proteins.  If they are both each others best
hit, then they are orthologous, and you can safely make a two column entry
for the maker_map_ids input (i.e. maker-gene-1 translates into smug1).

—Carson


From:  Daniel Ence <dence at genetics.utah.edu>
Date:  Friday, March 14, 2014 at 11:32 AM
To:  Janna Fierst <jfierst at uoregon.edu>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] associating gene names between related strains

Hi Janna, So do you have one strain that you want to use as the reference
for all the others? There's a script that comes with MAKER called
maker_map_ids that lets you use a common prefix or suffix for entries in a
fasta file from one strain and then use est_forward to use that ID in the
gene models for the other species.

Let me know if that's not what you're looking for,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Janna
Fierst [jfierst at uoregon.edu]
Sent: Friday, March 14, 2014 10:06 AM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] associating gene names between related strains

Hi,

we are assembling and annotating genomes for several related strains of
Caenorhabditis worms and I was wondering if there is a way to coordinate the
gene naming so that orthologs between species can be associated by name. I
have been playing around a little with the est_forward option but can't
figure out a good system/workflow that preserves names but still uses the
strain-specific RNA-Seq EST set for the actual gene models. Thanks! -Janna
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