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Nucleic Acids Research, Vol 25, Issue 22 4570-4580, Copyright © 1997 by Oxford University Press

ARTICLES

RAGA: RNA sequence alignment by genetic algorithm

C Notredame, EA O'Brien and DG Higgins
EMBL Outstation-The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. cedric.notredame@ebi.ac.uk

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).
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