In article <Pine.3.89.1.3.9612101029.A15858-0100000 at indycc1.agri.huji.ac.il>,
michar at INDYCC1.AGRI.HUJI.AC.IL (MIcha Ron) writes:
>Dear netters,
>>I have a question about GCG software. How do I create a new subset of
>sequences from an output of stringsearch. I would like to do a fasta
>search with all the output sequences recieved from the stringsearch.
Like lookup, stringsearch gives you a file of sequence names (FOSN)
formated output. So you can use fasta as follow :
--
fasta my_sequence
(...)
Search for query in what sequence(s) (* SwissProt:* *) ? @my_subset.strings
---
the @ says to GCG that this is a FOSN file, and GCG will take all the
sequences to make the search . You don't need to create a database,
nor to copy all the sequences (no need of disk space).
Ciao,
Francois.
--
Francois Jeanmougin
Service de bioinformatique / bioinformatics service
IGBMC BP 163 67404 Illkirch France
tel :(France) 03 88 65 32 71 / (international) (+33) 3 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr
"C'est pas parcequ'on monte au banc, qu'il faut descendre a jeun." (Thiefaine)
