[EMBOSS] Question regarding dbxflat

pmr at ebi.ac.uk pmr at ebi.ac.uk
Tue Oct 17 16:23:03 UTC 2006

Hi Jean,

> If I specify 'acc, id' while indexing, will the 'Definition' line be
> indexed or not? What about 'acc, id, des' ? In other words, I would like
> to know which programs in EMBOSS will not work if I don't specify 'des'
> while indexing.
> Some programs in EMBOSS such as 'coderet' require feature table. If I only
> index 'acc, id', will coderet work when user specify 'genbank:xxxxx' ?
> I guess all I am trying to ask is what programs will stop working if I
> only accept default 'acc, id' fields.

The dbxflat fields only affect queries (do you want to search by
dbname-des: or dbname-gi: when you look for sequences).

Retrieval is the same once an entry has been found - you can return all
txt for entret, features for coderet, and os on as usual.

By default only the id and acc lines will be indexed.

We found a problem with one database that had no accessions (pdb as a
fasta file indexed with dbxfasta) so the next release will have an option
to turn off accession searches in the database definition and we may add
an option to skip accession indexing.


Peter Rice

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