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

[Bob Freeman]

Thanks, all, for the *extremely* helpful suggestions. This will save  
me greatly in personal and compute time!!

I am poised to run MAKER to generate additional gene models to  
complement those generated from Baylor -- I may contact Carson and  
Mark separately with some very specific questions.

Best,
Bob

On Aug 14, 2009, at 6:03 PM, Carson Holt wrote:

>
> >>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.
>
> MAKER runs both blast and exonerate internally so it takes care of  
> this for you.
>
>
> >>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.
>
> MAKER can do this too. MAKER can run gene-finders like snap,  
> genemark, augustus, fgenesh for you.  In addition, MAKER also  
> produces evidence informed “hints” based on the EST and protein  
> alignments as well as mRNAs from closely related species.  MAKER  
> then talks to the gene predictors using the hints and causes them to  
> produce even better gene models.  MAKER will also revise these gene  
> models to include five and three prime UTRs when there is support  
> from EST evidence.
>
> MAKER will also run other programs for you like RepeatMasker if you  
> choose.  There are also tools for running InterProScan (a protein  
> domain finder), as well as tools for automatically assigning GO  
> functional terms and putative gene functions to each new gene  
> prediction.
>
> The newest revision of MAKER also comes with a handy maker2chado  
> script that will auto-load all MAKER produced GFF3 files into a new  
> or pre-existing chado database for you.
>
> Carson
>
>
>
> On 8/14/09 3:31 PM, "Don Gilbert" <gilbertd at cricket.bio.indiana.edu>  
> wrote:
>
>
>
>
> 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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>
>

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2293, vox

When choosing between two evils I always take the one I've never tried  
before. -- Mae West, Klondike Annie



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