blast on srs5.1

Thure Etzold etzold at ebi.ac.uk
Thu Jan 15 08:49:09 EST 1998


Francois Jeanmougin wrote:

> In article <884798805.425590801 at dejanews.com>,
>         Tim Dudgeon <dudgeon at britbio.co.uk> writes:
> > I've come across the solution to a previously posted message about blast
> > output not being correctly parsed.
>
>         I think it's not only an expected GCG ouput, it is also because
> different version of blast gives different output. We experienced such
> problems with DBWatcher...
>         If I remember correctly, Fred found a way to parse easily
> both outputs, but, Fred is out this week, so he will confirm next
> week if I'm right.

The BLAST parser in the SRS distribution is for an older version of BLAST. I
would be really grateful for suggestions on a syntax that is suitable for
different
versions.  We use here at EBI indeed the GCG tools to generate the databanks
in
FASTA format. The parser that reads the title line of each BLAST entry should
be able to read a variety of formats but there is no way of telling whether
entry
name or accession number comes first.

Thure





More information about the Bio-srs mailing list