[Bioperl-l] NCBI BLAST results parsing

Chris Fields cjfields at uiuc.edu
Thu Jun 8 09:12:23 EDT 2006


I would say, based on previous responses, update to the latest CVS  
(bioperl-live).  You could also try updating  
Bio::Tools::Run::RemoteBlast.pm and Bio::SearchIO::blast.pm if you  
don't want to update the entire toolkit.  Running these with BLAST  
2.2.14 output seems to work fine.

Though this is the likely fix, if you have additional problems next  
time please make sure to include more information.  We have no idea  
what OS, bioperl version, perl version you are running.  And a code  
snippet and bug description would be nice (i.e. "it doesn't work" -  
not a good description; "the script freezes" is a little more  
informative).

Chris

On Jun 8, 2006, at 6:38 AM, John Mifsud wrote:

> Dear all,
>
> Firstly I hope this is the right email list to write to!
>
> Secondly, I have a little program that parses the BLAST results i  
> have got
> running remotely to the NCBI server and takes out all the hit  
> sequences and
> converts them to FASTA format.
>
> Now when using BROAD BLAST and getting results this works fine  
> (tblastn ver
> 2.2.9). However, NCBI have just updated their BLAST server (to  
> 2.2.14) and
> the output is different and the parsing no longer works. I was  
> wondering if
> anyone knew of a new SearchIO module / script that is designed to  
> blast the
> updated NCBI BLAST output?
>
> Thanks for your time,
>
>
> John
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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