Fast sequence alignment algorithm using bloom filters

Abstract

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 NeedlemanWunsch 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.

Filtering technique for high speed database sequence comparison

“…This may open new era in database comparison applications. The crux of our technique is that it may be applied in conjunction with the previous state-of-the-art methods (as in [11] and [10]) to further improve their time performance. The rest of the paper is organized as follows.…”

“…Their method aligns the sessions in an average time gain of 35.84% over the conventional dynamic programming Needleman-Wunsch method. In [10], the authors presented fast algorithm for sequence alignment using Bloom filters which is used in web searching. They implemented their algorithm and compared it with the Needleman-Wunsch method.…”