Re: protein-database
Steffen Moeller <moeller@pzr3.pzr.uni-rostock.de> wrote:
> Hello Richard, hello Frank,
>>, nothing of great usefulness
> This depends on how you read the original request. What was asked for on
> some meta level is the supported update of standard databases in
> bioinformatics. This implies the definition of respective locations
> and a naming scheme for the downloaded files that come in so many
> different formats. We do not have that.
I also had this thought last evening.
> If we had this, though, all the other packages like EMBOSS, BioPerl or blast
> could be rendered much more powerful by reducing overhead for the
> administrators. Maybe we want a file in /etc that defines the location
> of the databases which may be anywhere in the local network or a
> a web service for the retrieval of individual entries which would then not be
> usable for search tools. Or are there already web services that do blast
> searches? Probably.
On the web there are some publically available,
http://www.ebi.ac.uk/blast2/
http://www.expasy.org/cgi-bin/BLASTEMBnet-CH.pl
But I do not know whether the web interface part is free software, or
whether it is available at all (and not just a local "hack").
Regards, Frank
--
Frank Küster
Inst. f. Biochemie der Univ. Zürich
Debian Developer
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