[Bioperl-l] extracting coding sequence from BLAST

Jason Stajich jason at bioperl.org
Fri Apr 13 16:47:50 EDT 2007


Hi -

There are some tools that do this for you -- I've listed a few from a  
google search or from what I remember reading.  It would be great If  
you (and others!) are willing to contribute a little of the info of  
what you find that works for you to the wiki, that would be great as  
well.   A little HOWTO would be cool - here or on openwetware.org.

Prot4EST http://zeldia.cap.ed.ac.uk/bioinformatics/prot4EST/index.shtml
EST-PAC:  doi: http://dx.doi.org/10.1186/1751-0473-1-2

Ewan Birney's estwise as part of wise package also can help if you  
have a likely protein from BLAST you want to align to the est -  
estwise can handle frameshifts, but can be too slow for some people.   
Exonerate's protein2dna model may also work here, but I haven't tried  
it.

-jason
On Apr 13, 2007, at 1:20 PM, Thiago Venancio wrote:

> 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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>> Bioperl-l at lists.open-bio.org
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>>
>>
>> --
>> Jason Stajich
>> jason at bioperl.org
>> http://jason.open-bio.org/
>>
>>
>>

--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/




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