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

[kokwei <kok...@gm...>]

Thanks for your information. I am thinking the reference proteins I used 
as database are conserved in their gene model, so hoping that with the 
blast result against database will predict the "real start" (with 
reference) instead of based on ab initio which might have false 
prediction for start codon. With the current protein blast alignment, it 
will pinned to the closest start codon upstream, but the "real start" 
might be even more upstream.

Can I have your opinion on this based on your experience with the 
optimization? Thanks.

On 2/7/2013 3:36 AM, Lee Katz wrote:
> 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... 
> <mailto: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.