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© Oxford University Press

A global approach for contig construction

A. Gleizes 1,1,2 and A. Hénaut 1,1

1Centre de Génétique Moléculaire du CNRS 91198 Gif sur Yvette cedex
2GENOMIC SA 441 route de la Combe 74 160 Collonges sous Soléve, France

1Address for correspondencer

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.

Received on October 13, 1993; accepted on March 9, 1994

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