[BioPython] back-translation method for Seq object?

[Peter]

On Tue, Oct 21, 2008 at 3:45 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Bruce wrote:
>>>> Another case where it would be useful is that tools like TBLASTN gives
>>>> protein alignments so you must open the DNA sequence and find the DNA
>>>> region based on the protein alignment.
>
> Leighton:
>>> You could use TBLASTN output - which provides start and stop coordinates
>>> for the match on the subject sequence - to extract this directly, without the
>>> need for backtranslation.  Example output where subject coordinates give
>>> the match location below:
>>> ...
>
> Bruce's reply:
>> Exactly my point, where is the DNA sequence? Only if you have direct access
>> to the DNA sequence can you get it. Furthermore, the DNA sequence must be
>> exactly the same because any change in the coordinates screws it up.
>
> You should have the original query from when you ran the BLAST
> search, so using the co-ordinates given in the BLAST hit you can
> recover the original nucleotide query which gives this match.

Sorry - I was thinking of the wrong variant of BLAST.  As Leighton
pointed out, you would have to use fastacmd to extract the nucleotide
sequence of the match from the blast database (assuming you were
running stand alone blastall) or fetch it via its accession (if you
were running BLAST via the NCBI).

Peter