BUG FIX FOR PIMA-1.2 (Pattern-Induced Multi-sequence Alignment program)
AND PLSEARCH-4.1 (MBCRR's Pattern Library and Search tool)
During the recent upgrade of pima-1.0 to pima-1.2 and plsearch-4.0 to
plsearch-4.1 a bug was introduced into the alignment algorithm that
affects the alignment of gaps across from long runs of gap characters
(a rare enough occurrence such that it was not detected during program
testing, but a serious enough bug that users should pick-up the fix).
Corrected versions of PIMA and PLSEARCH (pima-1.22 and plsearch-4.2)
are now available via anonymous ftp from mbcrr.harvard.edu
(both packages are in the 'MBCRR-Package' sub-directory as compressed
tar files; be sure to use 'binary' mode when transferring).
*--------------------------------------------*------------------------------*
| Randall F. Smith | Phone: 713-798-4735 |
| Keck Center for Computational Mol. Biology | FAX: 713-790-1275 |
| and Dept. of Cell Biology | |
| Baylor College of Medicine | |
| One Baylor Plaza | Internet: rsmith at bcm.tmc.edu |
| Houston, TX 77030 USA | |
*--------------------------------------------*------------------------------*
The original PIMA-1.2 announcement follows:
******************************************************************
Announcing Rel. 1.2 of PIMA
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 vol 5, num 1 (should be in US libraries
this week; see also Smith and Smith, 1990, PNAS 87:118-122).
The multiple alignment algorithm:
(1) is based on a local (Smith-Waterman) rather
than global (Needleman-Wunch-Sellars) dynamic programming algo-
rithm;
(2) aligns sequences based on the pattern of conserved
sequence elements/domains common to the homologous sequences be-
ing aligned;
(3) represents gaps within a multiple alignment in a
simple and consistent manner;
(4) can employ secondary structure-dependent gap penal-
ties for use in structural modeling of new protein sequences
when the 3D-structure of one or more members of the sequence fam-
ily is known.
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 = 134.174.70.60; the package is in a single
compressed tar file called pima-1.2.tar.Z in the MBCRR-Package
sub-directory, and
-----------------------------------------------------------------------
Note: Temple and I have both moved recently:
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
Molecular Bio-Enginnering Research Center
Boston Univ., 36 Cummington St, Boston, MA 02115
tsmith at darwin.bu.edu
-----------------------------------------------------------------------
