Target-align

A Smith-Waterman-like alignment tool was developed in order to accurately predict miRNA targets. Dynamic programming was used to build a score matrix based on the complementarity of nucleotides in order to trace the optimal local alignments. Important parameters, such as maximum mismatches and maximum consecutive mismatches between miRNAs and their targets, were also used for filtering the optimal local alignments. Almost all of the parameters in this alignment tool can be adjusted by users. Target-align can identify multi-target sites as well potential for non-cleaved targets sites by change the default settings.