Abstract—This paper presents a new algorithm for searching short fragments of sequences in long DNA sequences. A short sequence (pattern) is searched in both DNA strands with a given maximal value of errors. Each DNA sequence (T) is preprocessed by compressing it using Burrows-Wheeler transform and wavelet tree. First, the pattern is divided into short words which overlap themselves, and then their positions in T are determined using FM-index. Connections between the words are searched under the assumption of an acceptable maximal error allowed. Experimental results indicate that the algorithm is highly effective and it outperforms a popular Basic Local Alignment Search Tool (BLAST) in case of searching for short sequences.

Index Terms—Approximate string matching, compressed index, wavelet tree

J. Kawulok is with the Institute of Informatics, Silesian University of Technology, Gliwice, Poland (e-mail: jolanta.kawulok@polsl.pl).

 

Cite:Jolanta Kawulok, "Approximate String Matching for Searching DNA Sequences," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 3, no. 2, pp. 145-148, 2013.