[EMBOSS] Problem indexing PDB fasta file

[simon andrews (BI)]

On 10 Apr 2006, at 10:12, Peter Rice wrote:

> 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.

If anyone's interested I've got a small perl script which reformats the 
PDB database into a more sensible format and sorts out the problems 
with case sensitive ids and a number of other odd conventions used in 
PDB.

I'm happy to supply a copy to anyone who wants it.

TTFN

Simon.
-- 
Simon Andrews PhD
Bioinformatics Dept.
The Babraham Institute

simon.andrews at bbsrc.ac.uk
+44 (0) 1223 496463