Fast algorithms for finding patterns in indeterminate and Arc-Annotated sequences

In this paper, we present efficient algorithms for finding indeterminate Arc-Annotated patterns in indeterminate Arc-Annotated references. Our algorithms run in O(m + mn/w) time where n and m are respectively the length of our reference and pattern strings and w is the size of our target machine word size. Here we have assumed the alphabet size to be constant, because, indeterminate Arc-Annotated sequences are used to model biological sequences. Clearly, for short patterns, our algorithms run in linear time and efficient algorithms for matching short patterns to reference genomes have huge applications in practical settings. We also perform some preliminary experiments that suggest that our algorithms run very fast in practice.