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© IRL Press

‘Size leap’ algorithm: an efficient extraction of the longest common motifs from a molecular sequence set. Application to the DNA sequence reconstruction

Anne Danckaert , Colombe Chappey and Serge Hazout *

Unité de Recherches Biomathématiques et Biostaistiques, INSERM U263, Université Paris 7 2 place Jussieu, 75251 Paris Cedex 05, France

*To whom reprint requests should be sent

We propose a new method, called ‘size leap’ algorithm, of search for motifs of maximum size and common to two fragments at least. It allows the creation of a reduced database of motifs from a set of sequences whose size obeys the series of Fibonacci numbers. The convenience lies in the efficiency of the motif extraction. It can be applied in the establishment of overlap regions for DNA sequence reconstruction and multiple alignment of biological sequences. The method of complete DNA sequence reconstruction by extraction of the longest motifs (‘anchor motifs’) is presented as an application of the size leap algorithm. The details of a reconstruction from three sequenced fragments are given as an example.

Received on February 12, 1991; accepted on February 15, 1991

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