Comput Appl Biosci. 1990 Oct;6(4):325-31.

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

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Département de Biochemie, Université de Montréal, Québec, Canada.

Abstract

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.

PMID:: 1701686; [PubMed - indexed for MEDLINE]

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