****************************************************************** 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 programing 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 modelling of new protein sequences when the 3D-structure of one or more members of the se- quence family 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@bcm.tmc.edu Temple F. Smith Molecular Bio-Enginnering Research Center Boston Univ., 36 Cummington St, Boston, MA 02115 tsmith@darwin.bu.edu -----------------------------------------------------------------------