databases strategies

[Peter Rice]

Robert Milius <milius at bscl.msi.umn.edu> writes:

>Now I want to be able to use EMBOSS on the same databases using
>the dbiblast utility. This program creates 4 files: acnum.hit, acnum.trg,
>entrynam.idx, and division.lkp. The problem is that if I run
>dbiblast for each db in the directory, they overwrite the ones that
>that were just created.
>
>I suppose I can create a separate directory for each db, and symlink
>the files into a common BLASTDB directory. Is there a more elegant
>solution I'm missing?

Possibly, yes!

You can build the index files in a separate directory (for each database).
Run dbiblast in the index directory, and tell it the database is
somewhere else.

The division.lkp file should include the source database directory,
and if I recall correctly the database specification in emboss.default
also lets you define the database and index directories to be
different.

We didn't pick the index file naming - it comes from Staden and the
EMBL/EBI CD-ROM indexing, and is also used by the Sanger Centre's
'efetch' utility program in acedb.

Of course it could be changed - one option would be to add the
database name to all the files somehow to make unique names. If you
only have EMBOSS it does not matter about the compatibility. If you
have Staden you would be using that for indexing and reusing the files
in EMBOSS.

Peter

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/