Byte-Aligned Pattern Matching in Encoded Genomic Sequences

In this article, we propose a novel pattern matching algorithm, called BAPM, that performs searching in the encoded genomic sequences. The algorithm works at the level of single bytes and it achieves sublinear performance on average. The preprocessing phase of the algorithm is linear with respect to the size of the searched pattern m. A simple O(m)-space data structure is used to store all factors (with a defined length) of the searched pattern. These factors are later searched during the searching phase which ensures sublinear time on average. Our algorithm significantly overcomes the state-of-the-art pattern matching algorithms in the locate time on middle and long patterns. Furthermore, it is able to cooperate very easily with the block q-gram inverted index. The block q-gram inverted index together with our pattern matching algorithm achieve superior results in terms of locate time to the current index data structures for less frequent patterns. We present experimental results using real genomic data. These results prove efficiency of our algorithm. 1998 ACM Subject Classification F.2.2 Pattern Matching