Efficient algorithms for folding and comparing nucleic acid sequences
1982
Dumas, J.P. | Ninio, J.
Fast algorithms for analysing sequence data are presented. An algorithm for strict homologies finds all common subsequences of length > 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 5S RNA folding.
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