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Bioinformatics Vol. 18 no. 90002 2002
Pages S44-S53
© 2002 Oxford University Press

A new distance measure for comparing sequence profiles based on path lengths along an entropy surface

Gary Benson

Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, USA

Received on April 8, 2002 ; accepted on June 15, 2002

We describe a new distance measure for comparing DNA sequence profiles. For this measure, columns in a multiple alignment are treated as character frequency vectors (sum of the frequencies equal to one). The distance between two vectors is based on minimum path length along an entropy surface. Path length is estimated using a random graph generated on the entropy surface and Dijkstra's algorithm for all shortest paths to a source. We use the new distance measure to analyze similarities within familes of tandem repeats in the C. elegans genome and show that this new measure gives more accurate refinement of family relationships than a method based on comparing consensus sequences.


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