RAGA: RNA sequence alignment by genetic algorithm

C Notredame
1997 Nucleic Acids Research  
We describe a new approach for accurately aligning two homologous RNA sequences when the secondary structure of one of them is known. To do so we developed two software packages, called RAGA and PRAGA, which use a genetic algorithm approach to optimize the alignments. RAGA is mainly an extension of SAGA, an earlier package for multiple protein sequence alignment. In PRAGA several genetic algorithms run in parallel and exchange individual solutions. This method allows us to optimize an objective
more » ... function that describes the quality of a RNA pairwise alignment, taking into account both primary and secondary structure, including pseudoknots. We report results obtained using PRAGA on nine test cases of pairs of eukaryotic small subunit rRNA sequence (nuclear and mitochondrial).
doi:10.1093/nar/25.22.4570 pmid:9358168 pmcid:PMC147093 fatcat:yze3xxoeajh27f2wz2gsnl5z6i