IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

EMBL to NBRF/GCG conversion, rel 2.2

Jack Leunissen jackl at caos.kun.nl
Fri May 19 03:28:10 EST 1995

Dear Collegues,

Release 2.2 of the program "EMBL2NBRF" is available. It converts EMBL flat
files into PIR/NBRF format, which can be used by most sequence analysis
programs, or packages like GCG.

New in the current release is the ability to perform "on the fly" splitting
of data files into the EMBL taxonomic division files. This is increasingly
important, considering the size of esp. the EST section in the EMBL updates:
on May 15th, the EST section alone carried over 100,000 entries, of a total
of 120,000 in the cumulative updates!

Here is an example for the README file:

% zcat cumulative.dat.Z | emb2nbrf -m -n emnew -s emnew.info -x --

which reads the (decompressed) data from standard input ("--"), splitting
the entries in the EMBL cumulative updates into their taxonomic division
files (-x), and naming them "emnew_ba", "emnew_est", etc. The progress of
the action is monitored (-m), and the summary is written to a file (-s).

A small C-shell script is also provided to create the GCG header files.

The program can be obtained by anonymous ftp to "ftp.caos.kun.nl", in the
directory "/pub/molbio/embl2nbrf".
 The URL = ftp://ftp/caos.kun.nl/pub/molbio/embl2nbrf/

Or send an e-mail to Jack Leunissen (jackl at caos.kun.nl).


      Jack A.M. Leunissen, Ph.D. | CAOS/CAMM Center, Univ. of Nijmegen
      Email: jackl at caos.kun.nl   | Toernooiveld
      Tel. : +31 80 65 22 48     | 6525 ED Nijmegen, The Netherlands
      Fax  : +31 80 65 29 77     | URL=http://www.caos.kun.nl/

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net