Journal Article

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

Gary Benson

in Bioinformatics

Volume 18, issue suppl_2, pages S44-S53
Published in print October 2002 | ISSN: 1367-4803
Published online October 2002 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/18.suppl_2.S44
A new distance measure for comparing sequence profiles
based on path lengths along an entropy surface

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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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Subjects: Bioinformatics and Computational Biology

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