Pima users

Randall Smith rsmith at kite.bcm.tmc.edu
Mon Aug 31 09:38:25 EST 1992

In article <1992Aug31.141838.202593 at uctvax.uct.ac.za>, rybicki at uctvax.uct.ac.za (Ed Rybicki) writes:
>I am very interested in any and all VAX software for multiple sequence
>alignment / phylogeny generation: please could some kind soul send me
>the info on PIMA (and how to get it)?

PIMA currently runs only under Unix, but here is the distribution info
for others who may be interested:

                         PIMA 1.22
     Pattern-Induced Multi-sequence Alignment Program

PIMA is a multiple sequence alignment program that uses a dynamic
programming-based pattern construction method to align a set of
homologous protein sequences (Smith, RF and Smith, TF, 1992, Protein
Engineering 5:35-41; see also Smith and Smith, 1990, PNAS 87:118-122).

The multiple alignment algorithm:

	(1) aligns sequences based on the pattern of conserved sequence
elements/domains common to the sequences being aligned;

	(2) represents gaps within a multiple alignment in a simple and
consistent manner;

	(3) can employ secondary structure-dependent gap penalties for
use in structural modelling of new protein sequences when the
3D-structure of one or more members of the sequence family is known.

	(4) is based on a local (Smith-Waterman) rather than global
(Needleman-Wunch-Sellars) dynamic programing algorithm;

The PIMA package is available free of charge to non-profit organ-
izations; a distribution fee and non-resale agreement is required for
commercial use.

Note: The PIMA package is currently a Unix-only implementation.

Copies can be obtained via INTERNET anonymous ftp to:
mbcrr.harvard.edu =; the package is in a single
compressed tar file called pima-1.22.tar.Z in the 'MBCRR-Package'

Randall F. Smith
Human Genome Center and Dept. of Cell Biology
Baylor College of Medicine, Houston TX  77096
rsmith at bcm.tmc.edu

Temple F. Smith
Bio-Molecular Enginnering Research Center
Boston Univ.,  36 Cummington St, Boston, MA 02115
tsmith at darwin.bu.edu

More information about the Bio-soft mailing list

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