RAGA: RNA sequence alignment by genetic algorithm

TitleRAGA: RNA sequence alignment by genetic algorithm
Publication TypeJournal Article
Year of Publication1997
AuthorsNotredame C, O'Brien EA, Higgins DG
JournalNucleic Acids Res
Date PublishedNov 15
Accession Number9358168
KeywordsAlgorithms, Animals, Base Sequence, Evaluation Studies as Topic, Humans, Molecular Sequence Data, Nucleic Acid Conformation, RNA, Ribosomal/ genetics, RNA/ genetics, Sequence Alignment/ methods, Software

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 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).