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.
The virion-extracted DNA ( M , 5 x lo6) of cauliflower mosaic virus (CaMV) has three singlestranded interruptions. The mapping of this DNA using eleven restriction endonucleases (HhaI, S a d , AvaI, PvuII, PstI, XbaI, EcoRI, BglII, HincII, HpaII and HindII + 111) is reported here. The existence of the three single-stranded breaks complicates the identification and the molecular weight determination of fragments produced by HpaII, HindIII and HindII + 111. Indeed the electrophoretic mobility of some fragments in which a single-stranded discontinuity is located is modified, and the fluorescence of ethidium bromide complexed with these fragments is reduced as compared to that observed for the other fragments existing in a molar ratio. These drawbacks were overcome by performing experiments of nick-translation of CaMV DNA with Eschevichia coli DNA polymerase I. From the data it follows that the CaMV DNA molecule bears 1 site for HhaI and Sac& 2 for AvaI and PvuII, 3 for PstI, 4 for XbaI, 5 for EcoRI, 6 for BglII and HincII, 11 for Abbreviations. CaMV, cauliflower mosaic virus; SV40, simian virus 40.
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