Fast sequence alignment algorithm using bloom filters

This paper presents a fast algorithm for sequence alignment in Biocomputing using Bloom filters. The idea behind this proposed method is comparing subsequence of incoming sequences with Bloom filter and discovering the matched subsequence. The sequence alignment problem has a large number of comparisons. According to the last successful experiences of useing Bloom filter in similar issues such as web search, it seems that using Bloom filter to solving this problem can be an appropriate solution. To evaluate the proposed algorithm, it has been implemented and compared to the Needleman-Wunsch method. Results show that in average, outpout quality is improved by 41%, memory usage by 84%, and response time by 52% compared to Needleman-Wunsch method are improved. In addition, for real samples, output quality is almost equivalent, memory usage is improved by 95% and response time by 40% compared to the Needleman-Wunsch method.