Multithreaded implementation of a biomolecular sequence alignment algorithm-software/information technology

Abstract

This paper describes a parallel implementation of a sequence alignment algorithm for biomolecular sequence analysis. It uses multiple threaded programming for the most time consuming functions and works in X Window based interactive systems. Its sequence alignment operations include Pairwise Alignment, Star Alignment, Phylogeny Reconstruction and Generalized Tree Alignment. Both of fast and optimal modes are provided. The algorithms for Phylogeny Reconstruction, Generalized Tree Alignment, and Tree Alignment are based on heuristic stepwise addition and internal node sequence alignment induction methods.PTAR can be used for DNA, RNA, and PRO-TEIN sequence analysis. In general, the system can carry out the alignments for any sequences composed of characters a-z and A-Z.

An enhanced algorithm for multiple sequence alignment of protein sequences using genetic algorithm

“…It aims to infer clues about the unknown sequence by inferring biological characteristics of the matched sequence. One of the most challenging tasks in sequence alignment is its repetitive and time-consuming alignment matrix computations (Weiwei and Sanzheng, 2000[ 67 ]).…”