| Bioinformatics is a new science field. Research in this field involves multi-disciplines such as biology, computer science, mathematics, etc. Bioinformatics is subject to expose the biological signification of large amount of biological data and explore the mystery of life activities. Sequence alignment is a basic information disposal method in Bioinformatics. It is useful for discovering functional, structural, and evolutionary information in DNA and protein sequences .Because sequence data increase rapidly in biology sequence database, it is very exigent to develop algorithms that have high biology sensitivity and efficiency. Pairwise sequence alignment algorithms of Bioinformatics are studied in this paper. The main contents and production can be briefly summarized as follows:1. Based on fast pairwise sequence alignment algorithm named as Ukkonen, a high efficient applied global pairwise sequence alignment algorithm is presented in this paper. The algorithm used the memory method of FA (Fast Alignment) algorithm for reference. The FA algorithm records element's origin relation while computing score matrix. And the algorithm adoped the Checkpoint technology to obtain some Checkpoint Points in replacement matrix.2. Several classic pairwise sequence alignment algorithm were analysized. These algorithms were offered contrast experiment condition for the pairwise sequence alignment algorithm presented in this paper.3. After analyzing BLAST algorithm, based on method of sequence being divided, a novel parallel algorithm of pairwise sequence alignment is presented. The testing results indicate that the proposed algorithm is of high efficiency.4. On the basis of the sequence alignment algorithm presented in this paper, a sequence alignment software system was designed and implemented.The novel algorithms are better than traditional algorithms in sentivity and computing efficiency. The software system based on these algorithms can offer sustainment for bioinfromatics research . |
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