[maker-devel] associating gene names between related strains

[Janna Fierst]

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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