Re: [Cg-pipeline-users] prediction - blastSeqs

[Lee K. <ls...@gm...>]

It looks like you are correct.  Over the last couple of years, I optimized
a few different things and I guess I obviated that subroutine!

Yes, run_prediction will run GeneMark and Glimmer3, and combine with blast,
making a high-confidence set of genes.  To see a graphical representation
and explanation of our combining strategy, please see our 2010 paper:
http://bioinformatics.oxfordjournals.org/content/26/15/1819.full


On Mon, Jul 1, 2013 at 12:49 PM, kokwei <kok...@gm...> wrote:

>
> Hi,
>
> I noticed that during execution of pipeline with command <run_pipeline
> predict -p project>, the module "sub blastSeqs($$$) {" at line 1817 is
> not executed. Is that normal or only happen in my case? Attached the log
> of the prediction for your reference.
>
> I guess that module will do the blast of the contig/scaffolds sequences
> against the database selected and output the homology based gene model
> to combine with other ab initio gene model by glimmer and genemark,
> which is what I need and hope that this can be solved.
>
> Thanks.
>
>
>
>
>
>


-- 
Lee Katz, Ph.D.