DIRECTORY OF MOLECULAR BIOLOGY SOFTWARE


	(2023)
Publisher:	Dr. Temple F. Smith, Director
	Molecular Biology Computer 
		Research Resource, LG-127
	Dana-Farber Cancer Institute
	44 Binney Street
	Boston, MA  02115, USA.
	Telephone: +1 617 732 3746
	Fax:  +1 617 735 8653
	E:mail:  tsmith@mbcrr.harvard.edu

Product Name:	PIMA  (Version 1.0)

Distributor:	As above.

Summary:	Pattern-Induced Multi-sequence Alignment program employing 
	secondary structure-dependent gap penalties for protein modelling.

Computer
Requirements:	Unix:	Unix Workstation; Unix OS; 16 Mb memory

Product	PIMA is a multiple sequence alignment program that uses a dynamic 
Description:	programming-based pattern construction method (Smith, RF and Smith, 
	TF, PNAS 87:118-122, 1990) to align a set of homologous protein 
	sequences.  The multiple alignment algorithm used incorporates several 
	unique features: 1) it is based on a local (Smith-Waterman), rather than 
	global (Needleman-Wunch-Sellars), dynamic programing algorithm; 2) 
	alignments are based on the pattern of conserved sequence elements/ 
	domains common to the homologous.sequences being aligned; and 3) gaps 
	within a multiple alignment are represented in a simple and consistent 
	manner.  The program can also employ secondary structure-dependent gap 
	penalties for use in comparitive structural modelling of new protein 
	sequences when the 3D-structure of one or more members of the 
	sequence family is known.

Pricing:	Free of charge to non-profit organizations.
	Available electronically via Internet anonymous ftp to: mbcrr.harvard.edu
	A distribution fee and non-resale agreement is required for commercial use.

Support:	Electronic mail to rsmith@mbcrr.harvard.edu

Reviews:	None.

Respondent's
name:	Randall F. Smith, Ph.D.
	Research Associate, MBCRR