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Rapid and sensitive dot-matrix methods for genome analysis
1Rapid and Sensitive Dot-matrix Methods for Genome Analysis
Authors:
Yue Huang* and Ling Zhang
Address:
Lynnon Corporation, 116 rue du Milicien, Vaudreuil-Dorion, Quebec, Canada, J7V 9M4
Phone: 1-450-455-4894
Fax: 1-450-455-4269
*To whom correspondence should be addressed
Bioinformatics Advance Access published February 5, 2004
Copyright (c) 2004 Oxford University Press
2Abstract
Motivation: Dot-matrix plots are widely used for similarity analysis of biological sequences. Many
algorithms and computer software tools have been developed for this purpose. Though some of these
tools have been reported to handle sequences of a few hundred kilobases, analysis of genome
sequences with a length of 10 megabases on a microcomputer is still impractical due to long execution
time and computer memory requirement.
Results: Two dot-matrix comparison methods have been developed for analysis of large sequences. The
methods initially locate similarity regions between two sequences using a fast word search algorithm,
followed with an explicit comparison on these regions. Since the initial screening removes most of
random matches, the computing time is substantially reduced. The methods produce high quality dot-
matrix plots with low background noise. Space requirements are linear, so the algorithms can be used for
comparison of genome size sequences. Computing speed may be affected by highly repetitive sequence
structures of eukaryote genomes. A dot-matrix plot of Yeast genome (12 megabases) with both strands
was generated in 80 seconds with a 1GHz personal computer.
Availability: The implementation of the described methods in C language is available at
/dotplot/index.html.
Contact: yhuang@
Running title:
Dot-matrix methods for genome analysis
Keywords:
Genome analysis; dot-matrix; algorithm; fast search; DNA; sequence analysis
3Introduction
Dot-matrix analysis is an efficient method to search for similarities between two sequences (Gibbs and
McIntyre 1970, Argos 1987, Risler et a
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