SA-REPC: sequence alignment with regular expression path constraint

In this paper, we define a novel variation on the constrained sequence alignment problem, the Sequence Alignment with Regular Expression Path Constraint problem, in which the constraint is given in the form of a regular expression. Our definition extends and generalizes the existing definitions of alignment-path constrained sequence alignments to the expressive power of regular expressions. We give a solution for the new variation of the problem and demonstrate its application to integrate microRNA-target interaction patterns into the target prediction computation. Our approach can serve as an efficient filter for more computationally demanding target prediction filtration algorithms. We compare our implementation for the SA-REPC problem, cAlign, to other microRNA target prediction algorithms.