Extracting info from Blast results

S.W. Rasmussen swr at crc.dk
Sat Nov 20 11:54:48 EST 1999


Hi Hector,

DNATools has an unattended mail-blast function which processes the returned
result and inserts selected parts of it in the headers of the query sequences.
>From such annotated sequences you can display various types of sequence lists,
including specific lines of the headers (e.g. discription lines 1 - 5 which
includes the gi| information). The lists can be saved and probably parsed into a
spreadsheet. Well this was not exactly what you asked for, but may take you a
bit of the way in case there are no better suggestions.

Regards

Soeren

You find DNATools at http://www.crc.dk/phys/dnatools.htm

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

-- 
Soeren W. Rasmussen, Dr. scient.
Department of Physiology
Carlsberg Laboratory
Copenhagen, Denmark
swr at crc.dk, http://www.crc.dk/phys





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