Rep : how to extend gcg program to work on my personal sequences?

Mathew Woodwark mathew.woodwark at bbsrc.ac.uk
Thu Jan 18 06:40:15 EST 1996

"FERRAN,edgardo" <Edgardo.FERRAN at TLS1.elfsanofi.fr> (Tel\(poste582\)) wrote:
>Dr. Chyh-Chong Chuang has wrote
>> Dear netters:
>> 	Does some one has the experience to extend gcg program to work on 
>> personal sequences? This is the same to 'create' a personal database, 
>> did any one has done that?
>You may 'create' a personal database with the GCG-command dataset. For


>Edgardo Ferran
>Sanofi Recherche
>e-mail: edgardo.ferran at tls1.elfsanofi.fr

Dataset is a good answer, but here's another suggestion. 
If you don't have too many sequences, or expect to add to your set of sequences on a 
regular basis, I find it easier to keep a file of sequence names up to date. You can 
create this with a directory command and use it like a database. To make a file of 
sequence names (list file) under unix, simply pipe the output of an ls command to a 
file, eg a list file of all the sequences in your directory ending in .seq

ls *.seq > seq.fil

and then, to use this with, say, fasta, where you would specify a datalibrary 
(eg: genembl:*), type @seq.fil

(Under vms, (well *I* still have to use it!) the same thing is accomplished by 
$ dir/col=1/out=seq.fil *.seq )

When you add new sequences to your set, you simply recreate your file of sequence 
names. You can run dataset -append, but it takes longer.

Just my opinion. 



Dr Mathew Woodwark		            mathew.woodwark at bbsrc.ac.uk
Molecular Biology Software Support          Tel: 01582 762271
BBSRC Computing Centre                      Fax: 01582 761710
West Common, Harpenden
Hertfordshire, AL5 2JE, UK

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