searching local databases

[David Martin]

On Fri, 22 Feb 2002, Charles Plessy wrote:

> Hello,
>
> In GCG, i used to make a local blast database from a few hundred of
> sequences coming from a screen (for example), in order to be able to
> use gcg's databese searching tools on it.
>
> With emboss, i have built a local index of fasta files and modified my
> ~/.embossrc so that i can access them with the db:ID syntax.
>
> I am now stuck. Could anyone point me to ressources explaining how I
> can install fasta or blast on my linux, and how to instruct those guys
> to use my homemade emboss fasta database??

I have a tutorial to do just this.. There are a few slightly misleading
bits in it (section ordering mostly) but otherwise it is fine.

It doesn't cover installing BLAST, use the readme from NCBI for that.

those who are interested can email me for a copy (pdf). It requires NCBI
Blast and EMBOSS with the Swissprot database installed.

..d


>
> Thank you,
>
> Charles
>

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David Martin PhD
Bioinformatics Scientific Officer
Wellcome Trust Biocentre, Dundee
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