[maker-devel] Mapping gene names

[Carson Holt]

There is a way.  It’s not a standard option and it’s undocumented, but if
you add est_forward=1 to the maker_opts.ctl file, then it will do just that.
The option won’t already be there so you’ll have to type it in.

There is also a feature designed to work with this option.  If you add tags
to your fasta headers, those can be used to guide the mapping and naming.
For example, gene_id=<some_gene>  will ensure different isoforms that share
a common gene_id get clustered into the same gene, and
maker_coor=chr1:1-10000 in the fasta header will force a particular sequence
to only be mapped against chr1 within the range of 1-10000 bp  and just
using maker_coor=chr1 will force it to only be mapped against chr1.

This is an undocumented way to remap genes onto new assemblies using blast
alignments of earlier transcript or protein annotations as a guide.

—Carson




From:  Shaun Jackman <sjackman at gmail.com>
Reply-To:  Shaun Jackman <sjackman at gmail.com>
Date:  Tuesday, February 25, 2014 at 5:06 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Mapping gene names

Hi,

I’m annotating a genome using a closely related genome from Genbank, using
the .frn (RNA) and .faa (protein) files from Genbank as evidence to annotate
my genome. I’ve run Maker, and the annotation seems to have worked well. Is
it possible to map the names of the genes from the related species to my
annotation? I see the map_forward option, which applies to the model_gff
parameter. Is there a similar option for est and protein?

maker_opts.ctl
est=NC_123456.frn
protein=NC_123456.faa
est2genome=1
protein2genome=1
Thanks,
Shaun
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