[EMBOSS] [Mrs-user] case sensitive identifiers

Peter Rice pmr at ebi.ac.uk
Thu Sep 28 14:32:36 UTC 2006

Guy Bottu wrote:
> My idea is to let the MRS parser store 1fnt_aLC
> (LC means lowercase) as identifier. A user can then search for the 
> sequence he needs in MRS and in EMBOSS (if the EMBOSS installation uses 
> MRS as databank access mechanism) ask for the sequence pdbprot:1fnt_alc.
> This would of course also work with 1fnt_a_12835 but it avoids the use of 
> a meaningless and irreproducible number. Anybody a comment ?

Not a general solution, but for PDB chains you could use an extra 
underscore for the lower case ones.

For EMBOSS .... well, we could play with the way databases work. Not all 
access methods allow case sensitive searching, but we could fetch all 
entries and try to reject those that do not match. This would need 
something in the EMBOSS id. We already allow modifiers after the id to 
set sequence ranges pdbprot:1fbt_a[1:20] or we could add a qualifier 
-scasesensitive for all sequence inputs.


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