[Bioperl-l] extracting coding sequence from BLAST

Jason Stajich jason at bioperl.org
Fri Apr 13 16:05:42 EDT 2007


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
> -- 
> "The way to get started is to quit talking and begin doing."
>       Walt Disney
>
> ========================
> Thiago Motta Venancio, MSc
> PhD student in Bioinformatics
> University of Sao Paulo
> ========================
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--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/




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