A global approach for contig construction.
A program for assembling sequences by using a global approach has been developed. By successive steps, a more and more precise classification of DNA fragments permits the positioning of the sequences on the contig; after having detected the pairs of overlapping sequences, groups are formed such that all sequences in a group overlap. Sequences common to several groups enable the groups to be ordered in a series. Ambiguities in the order of groups can arise at this stage, due to the presence of repeated fragments; different solutions are then proposed. Putting the groups into order leads to a preclassification of sequences. The fragments are then aligned by group, by searching for words common to all sequences in the group, and using an algorithm of dynamic programming. A detailed example on a set of nine sequences accompanies the description of the method.
Gleizes
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Centre de Génétique Moléculaire du CNRS, Gif sur Yvette, France.
Hénaut
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D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D005821:Genetic Techniques; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods / Q000706:statistics & numerical data; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software
D018076:DNA, Complementary; D004247:DNA