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NRL-3D database into GCG format?

Reinhard Doelz doelz at comp.bioz.unibas.ch
Wed Jan 5 02:10:44 EST 1994


In article <1994Jan4.212503.1 at mscf.med.upenn.edu>, pathology at mscf.med.upenn.edu writes:
|> Can anyone comment on the ease of converting the NRL-3D database (amino acid 
|> sequence database of proteins in the Brookhaven Protein Databank) to a format 
|> suitable for GCG programs?  Any general advice on how to do the conversion?  
...

The use of such a database is fairly straightforward and easy to achieve.

The most convenient solution for you were to store the uncompressed 
database at some place, then invoke GCG and GCGSUPPORT. 
Run the program pirtogcg and it wil automatically do most of the 
work (.header and other auxiliary file creation). It will also write 
all the files (including a copy of .ref and .seq files) into 'pirdir'
where you will find them afterwards if you define 

(on VMS, in SITEUSERSPECS.COM:)

$ Assign/NoLog PIRDir:NRL_3D                                  NRL_3D

(on UNIX, in siteuserspecs:)

 name -q -s nrl3d      PIRDir:nrl_3d

Verify the database after rerunning gcg with the 'names' , 'fetch', 
'stringsearch (menu a)', and 'fasta' programs. 

The more 'advanced' way would be to create the header file manually
and run dbindex directly on the .ref and .seq files, followed by a 
seqcat. You might want to try the latter for subsequent releases. 

(BTW, the method above applies to all databases in PIR format; if you 
want to place it somewhere else than Pirdir redefine it with 

(on VMS) 
$ define pirdir mydisk:[mydirectory]

(on UNIX)
% name -s pirdir /my/disk

I have done similar work with the OWL database (from Daresbury) and 
the patchx database (from Munich). ) 

Hope this helps
Regards
Reinhard 

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