[EMBOSS] Problem indexing PDB fasta file

Peter Rice pmr at ebi.ac.uk
Mon Apr 10 05:12:00 EDT 2006

Enrique de Andres Saiz wrote:
> I have been looking the PDB fasta file and I see that, for the previous 
> warning, there are an entry whoose id is '1FNT_A' and another one whoose 
> id is '1FNT_a'. Then, this make me think that EMBOSS is 
> case-insensitive. Is this true? Are there any way to distinguish between 
> the two id's?

Yes, EMBOSS is case-insensitive. So is the Staden/EMBLCD indexing standard 
that dbifasta uses.

The standard also only allows one entry with each ID.

dbxfasta uses a new indexing format and can index both entries, but will still 
assume the names are the same (a search for 1FNT_A or 1FNT_a wil return both 
entries). Allowing indexing to be case-sensitive is possible in future, but 
can slow down searches. We will investigate.

Hope that helps,


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