A Web Server for Multi-objective Pairwise RNA Sequence Alignment with an Index for Selecting Accurate Alignments

The importance of non-coding RNAs and their informatics tools has grown for a decade due to a drastic increase of known non-coding RNAs. RNA sequence alignment is one of the most important technologies in such informatics tools. Recently, we have proposed a multi-objective genetic algorithm, Cofolga2mo, for obtaining an approximate set of weak Pareto optimal solutions for global pairwise RNA sequence alignment, where a sequence similarity and a secondary structure contribution are taken into account as objective functions. In the present study, we have developed a web server for obtaining RNA sequence alignments by Cofolga2mo and for assisting the decision making from the alignments. Furthermore, we introduced an index for reducing the number of alignments output by Cofolga2mo. As a result, we successfully reduced the maximum number of alignments for an input RNA sequence pair from fifty to ten without a significant loss of accurate alignments. By using the BRAliBase 2.1 benchmark dataset, we show that a set of alignments output by Cofolga2mo for an input RNA sequence pair, which has at most ten alignments, includes an accurate alignment compared to those of the previous mono-objective RNA sequence alignment programs.