[Bioperl-l] SearchIO , blastn and blastx

[Jason Stajich]

This is the expected behavior, blastn reports don't have a frame.  You are
not translating the dna into protein so there is no frame.  blastx (and
fastx) is a nucleotide versus protein db so in that case your query will
have a frame, but your hits will not since they are proteins.  In tblastn
(and tfastn) only the subjects will have a frame since it is a protein
query against a translated nucleotide db, and in tblastx (and tfastx) both
query and hit will have frames.


On Wed, 3 Apr 2002, David Vilanova wrote:

> Hello ,
> I've been trying to use SearchIO but I'm getting some problem while
> parsing.
>
> I don't reach to retrieve the Frame from a blastn report ????
> I use $hsp->frame but doesn't return the correct value.
>
> My script launches a blastn using standalone blast from ncbi (2.2.2). I
> use read_method = "blast" to parse with BLAST instead of Bplite.
> Afterwards I loop each hit and for each hit I loop through every hsp.
> Can someone explain how to retrieve the frame or the strand with
> SearchIO after running a blastn?
>
> Also ,the strange thing is that $hsp->frame  returns the correct value
> if I parse  a blastx report with the same script (just by changing the
> database and the program).
> Thanks.
>
> Ps: I can post my script if helps?
>
> David Vilanova
>
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>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu