databanks in PIR format

[Peter Rice]

Guy Bottu wrote:
> I have EMBOSS 2.0.0 and a databank in PIR format (the version in NBRF format is
> indexed under SRS). My emboss.default file contains :
> 
> DB pir_nr [ type: P format: nbrf comment: 'PIR nonredundant'
>             methodquery: srs dbalias: PIR_NR
>             methodall: direct dir: /seq/protein/flat file: pir_nr.seq
> ]
> 
> But this does not work. E.g.  seqret pir_nr:e69549  gives an output file 

This is because of problems in SRS converting PIR entries to PIR format.
This has been the same since the days of SRS 5, but I have passed it on to
the support guys here to take a look. Seems nobody has been retrieving PIR
entries in their original format.

For example, see PIR on the SRS 5 server at MIPS:

http://srs-mips.gsf.de/srs5bin/cgi-bin/wgetz?-id+2trYB1GreRI+-e+[PIR-ID:'E69549']

You can get queries to work with:

DB pir_nr [ type: P format: fasta comment: 'PIR nonredundant'
            methodquery: srsfasta dbalias: PIR_NR
            methodall: direct dir: /seq/protein/flat file: pir_nr.seq
]

... but the fasta format required for srsfasta will not let you work with
direct access to all entries.

srs access does getz -e

srsfasta access does getz -d -sf fasta

regards,

Peter

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723