[EMBOSS] Problem indexing PDB fasta file

Jon Ison jison at ebi.ac.uk
Fri Apr 7 11:34:24 EDT 2006

Hi Enrique

dbifasta will return just the first entry with a duplicated id.
The new dbxfasta will return all entries with the duplicated id.

dbifasta is indeed case-insensitive.   To make it case-sensitive,
you could change the 3 instances of "ajStrMatchCaseC" in dbifasta.c
to "ajStrMatchC", recompile and try again.  I don't think we'd want
to make that change in the distribution though.

Hope that helps.



> Hello,
> I'm trying to index the fasta file of the PDB database with dbifasta
> command and I get a lot of warnings as:
> Warning: Duplicate ID skipped: '1FNT_A' All hits will point to first ID
> found
> 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?
> Thanks in advance,
> Enrique.
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> EMBOSS at lists.open-bio.org
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