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findpatterns

Jack Leunissen jackl
Mon Sep 25 03:14:50 EST 1995


Tylzanowski Przemko <przemko> wrote:
>I have to search genpept for a pattern. Well, everything worked, I got my
>findpatterns.find file and now I am stuck. I have about 140 hits in about as
>many genes. I would like to pull all the sequences out and have a quick look
>but I don't knwo how to do that. Of coursde, I could do it by hand, but it
>would be a bit tedious, especially if with some other patterns I find more
>hits.
>So, my question is this, how could I, easily and painlessly, retrieve the
>sequences and comments in question. Subsequently I would like to put them into
>pileup or smething like that.

Use the "-names" (or "/names" on VMS) parameter, to write out all hits as a
file in the "file of sequencenames" format (a FOSN). Then use FETCH or 
TYPEDATA, or better still SRS to extract/view all data from the database(s).

The FOSN can also be used to throw the sequences in PILEUP.

Cheers,
Jack

-- 
      Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center, Univ. of Nijmegen
      Email: jackl at caos.kun.nl   | Toernooiveld
      Tel. : +31 24 365 22 48    | 6525 ED Nijmegen, The Netherlands
      Fax  : +31 24 365 29 77    | URL=http://www.caos.kun.nl/




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