An Improved Quick Algorithm for Aligning DNA/RNA Sequences

Biology sequence database search is an important problem for bioinformatics research. The main search software BLAST is based on the BYP algorithm[1]. In BYP, if the length of hit region is set long, it may lose similar appearance. Otherwise, there may be too many r-length regions from Aho-Corasik algorithm. Checking where exists any approximate alignments for the DNA or RNA sequence always spends much time, although the expected running time of BYP is linear. A new algorithm is proposed from the viewpoint of shorting the length and increasing the number of the regions, which can make most of the false r-length regions excluded. Thus the algorithm can align the DNA or RNA sequences quickly since the rate of real r- length regions is increased. Experimental results show that the proposed algorithm is computational efficient and achieves good performance.