[Bioperl-l] extracting coding sequence from BLAST

Thiago Venancio thiago.venancio at gmail.com
Fri Apr 13 16:20:32 EDT 2007


Thanks Jason.

I have a large dataset (assembled ESTs) and several BLASTX or TBLASTX
comparisons and want to extract some translated coding regions for further
multiple aligmnent and phylogenetic analysis.

Best.

Thiago

On 4/13/07, Jason Stajich <jason at bioperl.org> wrote:
>
> Depends on how far away the query protein is, but I don't trust BLAST for
> the actual alignment.  Find the boundaries, add a little slop, and refine
> the alignment of protein to genome with a good alignment program designed to
> like genewise or exonerate or even FASTX/Y.
> -jason
> On Apr 13, 2007, at 12:05 PM, Thiago Venancio wrote:
>
> Hi all.
>
> What is the best way to extract coding region from a nucleotide sequence
> based on a BLASTX or TBLASTX comparisons ?
>
> Thanks in advance.
>
> Thiago
>
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>
> --
> Jason Stajich
> jason at bioperl.org
> http://jason.open-bio.org/
>
>
>


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