Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA.
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.
Gautheret
D
D
Département de Biochemie, Université de Montréal, Québec, Canada.
Major
F
F
Cedergren
R
R
D000465:Algorithms; D000595:Amino Acid Sequence; D008838:Microcomputers; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012343:RNA, Transfer / Q000737:chemistry*; D012984:Software
D012313:RNA; D012343:RNA, Transfer