title: Efficient algorithms for folding and comparing nucleic acid sequences.
abstract: Fast algorithms for analysing sequence data are presented. An algorithm for strict homologies finds all common subsequences of length greater than or equal to 6 in two given sequences. With it, nucleic acid pieces five thousand nucleotides long can be compared in five seconds on CDC 6600. Secondary structure algorithms generate the N most stable secondary structures of an RNA molecule, taking into account all loop contributions, and the formation of all possible base-pairs in stems, including odd pairs (G.G., C.U., etc.). They allow a typical 100-nucleotide sequence to be analysed in 10 seconds. The homology and secondary structure programs are respectively illustrated with a comparison of two phage genomes, and a discussion of Drosophila melanogaster 55 RNA folding.
mesh_terms: D000818:Animals; D001483:Base Sequence; D003201:Computers; D004247:DNA; D004331:Drosophila melanogaster / Q000235:genetics; D009690:Nucleic Acid Conformation; D012313:RNA; D012367:RNA, Viral
chemical_list: D012367:RNA, Viral; D012313:RNA; D004247:DNA