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RAGA: RNA sequence alignment by genetic algorithm.

ABSTRACT: 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).

SUBMITTER: Notredame C

PROVIDER: S-EPMC147093 | biostudies-other | 1997 Nov

REPOSITORIES: biostudies-other

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RAGA: RNA sequence alignment by genetic algorithm.

Notredame C C O'Brien E A EA Higgins D G DG

Nucleic acids research 19971101 22

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]

PMID: 9358168

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SAGA: sequence alignment by genetic algorithm.

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