Pattern similarity search in genomic sequences

Genomics, with the high amount of heterogeneous data that it is generating, is opening many interesting practical and theoretical computational problems; one of them is the search for a collections of genomic regions at given distances from each other, i.e., a pattern of genomic regions, along the whole genome. In this paper we present an optimized pattern-search algorithm able to find efficiently, within a large set of genomic data, genomic region sequences which are similar to a given pattern. We start with a base version of the problem, which is solved using dynamic programming enhanced with an efficient window-based technique; then, we extend the algorithm to more complex scenarios with practical applications in revealing interesting and unknown regions of the genome, thus, making it an important ingredient in supporting biological research. We apply our algorithm to enhancer detection, a relevant biological problem, showing that the method is both efficient and accurate.