databases

[Peter Rice]

w2hgcg at netscape.net wrote:
> 
> I am trying to learn how to set up emboss on my pc,
>I am running linux suse 7.3, and have some space on my HD,
> I would like to know  from where can I download a little database
> (no matter what this DB be about) so I can use it to learn to
> implement the emboss pack, I do not really care about what the
> DB be about because I only want it for learning how to set the
> emboss up, and see it runing on my pc, just one little thing I
> would need a not so big DB, let say for example some between
> 5 to 10 megs, or something like so, well thanks a lot in advance.

There are small databases included in EMBOSS in the test directory after
you unpack the release.

The EMBOSS developers use them to test database indexing and sequence
reading.

See directories:

test/data    (emrod (DNA) and swnew (protein) are in blast format)
test/embl    (*.dat for EMBL format, *.ref and *.seq for gcg format)
test/pir     (*.ref and *.seq for nbrf format)
test/swiss   (*.dat for swissprot format, 1 file)
test/swnew   (*.dat for swissprot format, 3 files)
test/wormpep (wormpep is in fasta and blast format)

If you use the emboss/emboss.default.template file to create your own
emboss.default file, change the definition of emboss_tempdata at the top to
point to your test directory and you can use the test databases as "tembl",
"tsw" and so on. The databases contain the sequences in the program
examples (see the web pages, or run the "tfm" program to see the
documentation).

You can also reindex these files yourself to test the dbi* programs and to
test writing your own DB definitions for emboss.default.

regards,

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723