[Gmod-help] RE: [maker-devel] [Gmod-gbrowse] Best practices for generating alignments for GBrowse...

[Mark Yandell]

>My basic outline for mapping related genes is to use BLAST for
>a coarse location, then exonerate for a refined mapping.
>Using just exonerate w/o pre-located genes is possible but
>you end up with a much large compute task and generally
>more gene mappings than you know what to do with.


Yep. This is basically what MAKER does-- and it will handle all of these tools eccentricities as well.

--mark

Mark Yandell
Associate Professor of Human Genetics
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707
________________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Don Gilbert [gilbertd at cricket.bio.indiana.edu]
Sent: Friday, August 14, 2009 3:31 PM
To: bob_freeman at hms.harvard.edu; help at gmod.org
Cc: maker-devel at yandell-lab.org; gmod-gbrowse at lists.sourceforge.net
Subject: Re: [maker-devel] [Gmod-gbrowse] Best practices for generating alignments for GBrowse...

Bob,

Here is my two-bits advice on your general questions of gene to genome
mapping tools.

>> Specifically, we'd like to load the following:
>> ESTs positioned against genomic scaffolds (same species)
>> BLAST? or a better program?

GMAP is the one I use and recommend for EST alignments,
but BLAT works, exonerate, BLAST and others also work.

>> Full-length mRNAs/clones (same species)
>> BLAST? or something better?

add exonerate here (maybe the older GeneWise). exonerate will give
you more complete gene/mRNA mappings than BLAST.

>> mRNAs from closely-related organisms for cross-species comparisons on gene
>> structure
add exonerate here

>> ?
>> proteins from closely-related organisms for cross-species comparisons on
>> gene structure
exonerate

My basic outline for mapping related genes is to use BLAST for
a coarse location, then exonerate for a refined mapping.
Using just exonerate w/o pre-located genes is possible but
you end up with a much large compute task and generally
more gene mappings than you know what to do with.

For your question of remapping to new assemblies, if the
MAKER or Flybase answers are not what you want, look at
UCSC genomes, and Jim Kent's software.  They do a lot
of that, mapping b/n assemblies.  The short answer is
if the assemblies don't change much then tools will
move annotations from one to the next.  If they do
change, you are generally better off re-running your
gene-finding, gene-mapping software.

-- Don

-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/

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