[maker-devel] associating gene names between related strains

[Carson Holt]

I'm glad we could help.

--Carson

From:  Janna Fierst <jfierst at uoregon.edu>
Date:  Friday, March 21, 2014 at 9:43 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Daniel Ence <dence at genetics.utah.edu>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] associating gene names between related strains

Hi,

I just wanted to say thanks for all your help- I did the reciprocal best
blast hits and then used the maker scripts (map_fasta_ids, map_gff_ids) to
associate names between strain assemblies/annotations. Worked perfectly!
-Janna


On Fri, Mar 14, 2014 at 11:02 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 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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