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GCG FETCH vs GenPept

Stuart M. Brown browns02 at mcrcr0.med.nyu.edu
Wed Apr 16 11:17:03 EST 1997


OK, once again GCG shows my glaring stupidity.

Why am I unable to FETCH sequences from my local database
that have GenPept accession numbers of the format: 192960

I like using WWW Entrez for text-based searching of sequences,
but the majority of protein sequences found in Entrez cannot be
FETCHED on my GCG system (for the most part I do not have this
probelm with DNA sequences).  

I am willing to switch from GenPept to TREMBEL as our database
of protein translations (supplement to Swissprot and PIR), but
I was similarly unable to retrieve these sequences from the 
EBI SRS server.  

Why are the accession numbers that GenBank uses in Entrez not
compatible with the accession numbers that GenBank uses in the
GenPept database that I get by FTP? or have I done something
wrong in the installation and set up of my GenPept database 
within GCG?  (it works fine for FASTA searches)

This boils down to the fact that I can FETCH a DNA sequence 
record that contains the protein translation in its annotation,
but I cannot find any way to retrieve that protein sequence as
a database record. So I am left cutting and pasting the protein
sequence into a text file - this solution does not scale for 
hundreds of sequences!

-- 
Stuart M. Brown, Molecular Biology Consultant 
NYU-MC Research Computing Resource, Dept. of Cell Biology
550 First Ave, New York, NY 10016
Phone: (212)263-7689  FAX: (212)263-8139



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