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© IRL Press

Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA

Daniel Gautheret , Francois Major 1 and Robert Cedergren *

Departément de Biochimie Canada
1Département d'Informatique et Recherche Operationnelle, Université de Montréal CP 6128, Succ. A, Montréal, Québec H3C 3J7, Canada

*To whom reprint requests should be sent

A convenient pattern-matching program using primary and higher-order structural features has been developed based on a ‘backtracking’ algorithm. A second implementation of the algorithm uses descriptors of structural features (including primary sequences) to align a list of homologous or highly similar sequences. An application of the pattern matcher to the search for tRNA and group I intron structural motifs in sequence data banks is presented. The design of a highly discriminate tRNA motif common to all cellular tRNAs and not found in a control sequence bank, was accomplished using the pattern matcher in conjunction with the alignment program.

Received on December 5, 1989; accepted on April 10, 1990

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