[Bioperl-l] NCBI BLAST results parsing

Sendu Bala sb at mrc-dunn.cam.ac.uk
Thu Jun 8 09:03:05 EDT 2006


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?

You'll probably need to get the latest SearchIO blast module from 
bioperl-live.
http://bioperl.org/wiki/Getting_BioPerl

If you're having difficulties with your setup, John, I can just send you 
the relevant file(s). Mail me (or Alan) privately for that.


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