Extracting info from Blast results

Patrick Durand durand at ncbi.nlm.nih.gov
Tue Nov 23 10:13:38 EST 1999


Hi,

one solution to your problem could be to use Octopus, a software I've written to
parse BLAST/FASTA outputs. Using Octopus, you can search for keywords, like 
"gi|" from your example, and create a new BLAST file containing only the
result of that search. More information on Octopus are available :

http://www.lmcp.jussieu.fr/~durand/HtmlDoc/software/octopus/octo_main.html


--Patrick



Hector Romero wrote:
> 
> Hi,
> I want to know if someone knows about any software capable of extracting
> only the gi| or header information from the output of standalone blast
> (is the same as all other outputs), and produce a kind of table with the
> query and subject gis or accesions.
> Actually I am searching orthologous genes, but working at the genomic
> level this turns out to be quite tedious.
> Thanks
> Hector





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