ANNOUNCE: PIMA Version 1.40

Brent Wiese brent at bcm.tmc.edu
Mon Aug 21 17:57:12 EST 1995


We are pleased to announce version 1.40 of PIMA, our Pattern-Induced
Multiple-sequence Alignment program (see RF Smith and TF Smith, 1992,
Protein Engng 5:35).

Some of the things worth noting about this new version are: A new
pattern alphabet representing 63 combinations of amino-acids is used
(see the man page [posted online as
http://dot.imgen.bcm.tmc.edu:9331/multi-align/Help/pima.html] or the
file 'doc/pima.help' for more information).  The alignment routine has
been enhanced to merge additional local alignments outside the region
of the highest scoring local alignment.  This version now supports
multiple sequence file formats, including IG, GenBank, NBRF, EMBL,
Fasta, and PIR.  Support for GDE (Generic Data Environment) is
provided (see the file 'etc/gde-menu').  Also portability and
robustness have been improved.

Source code can be obtained via ftp from gc.bcm.tmc.edu (128.249.26.6)
in the directory pub/software/pima under the name pima-1.40.tar.gz.
Pre-compiled binaries for selected platforms (solaris-2.3, sun4, osf1,
irix5) are also available (see the file 'README-binary').

This software should compile and run on most UNIX systems with an ANSI C
compiler.

**Note** : If you have World Wide Web access, there is no need to
obtain the source code.  PIMA alignments can be run directly from our
WWW Site (using the BCM Search Launcher):
  http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html
Our new batch client for Unix and Macs can also be
used to perform PIMA, CLUSTAL-W, and MAP multiple alignments, see:
  http://dot.imgen.bcm.tmc.edu:9331/seq-search/batch-client-announce.html


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Brent Wiese and Randall Smith
Human Genome Center
Department of Molecular and Human Genetics
Baylor College of Medicine, Houston, TX  77030  USA

{brent,rsmith}@bcm.tmc.edu; 713-798-4735; FAX: 713-798-5386
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