(93) Multiple Sequence Alignment by Parallel Iterative Improvement Method (KLIC version)

	Machine:     UNIX Machine
	Environment: UNIX, KLIC
	Language:    KL1, C
	Source Code: 3 MB
	Documents:   Manual (English / Japanese)

Overview

This system partially improves temporary alignment in an iterative way, and can effectively achieve high-quality alignment as a result. (KLIC version)

Features

Partial optimization modules by dynamic programming. Each of the modules, written in KL1 on KLIC or in C language, is executed on a slave processing element.
Parallel execution control module. This module, written in KL1 on KLIC, works on a master processing element.
Miscellaneous sequential modules. These modules, written in C language, are available for the performance evaluation of parallel processing.

Function

Multiple branches of a search tree in this combinatorial problem are evaluated in parallel by using many processing elements in each iteration.

The heuristic method, ``Restricted Partitioning Technique,'' prunes a large number of branches in the search tree and makes it possible to solve the combinatorial problem in a practical amount of time.

FTP

Multiple Sequence Alignment by Parallel Iterative Improvement Method (KLIC version) [626K]

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