Fasta format to GCG DATALibrary

Conrad Halling chhall at bb1t.monsanto.com
Thu Mar 3 17:49:58 EST 1994

In article <2l2t56$bh4 at csi0.csi.UOttawa.CA>, sbaird at mgcheo.med.uottawa.ca
(Stephen Baird) wrote:

> I have been unsuccessfully trying to convert databases
> formatted in the FASTA format to a GCG Data library. I've
> tried using readseq with the -a option and converting it
> to a genbank format and then using genbanktogcg to convert
> that file to a gcg data library. Although files are made, the fasta
> program can not sucessfully use them. The two databases that I have
> been having trouble with are the tfdaa (transcription factor
> database) and the GCRDb (G-protein coupled receptor database).
> Does anyone do this conversion and possibly even add more
> descriptive data to the database than comes with the
> fasta format?

GenBankToGCG works only with the files distributed from GenBank, not on a
collection of individual GenBank-format files.  What you need to do is
use ReadSeq to convert your FASTA-format files to GCG-format files.
Then use the DataSet program to build a library that can be searched
using StringSearch, Fetch, and FASTA.
Conrad Halling
Computational Molecular Biologist
Monsanto Co., St. Louis

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