[maker-devel] Mapping gene names

[Carson Holt]

One more note.  When using this option, the score column of mRNA features
will represent how completely this gene matches the source EST/protein
(fraction coverage multiplied by % identity).  So a value of 100 means there
is perfect match.  This way if the same transcript maps to multiple
locations, then you can identify which locations is the closest match (also
works for identifying likly orthologs vs. paralogs).

—Carson


From:  Carson Holt <carsonhh at gmail.com>
Date:  Tuesday, February 25, 2014 at 5:58 PM
To:  Shaun Jackman <sjackman at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Mapping gene names

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
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m
aker-devel_yandell-lab.org


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140225/bc343f94/attachment-0003.html>