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Bioinformatics Advance Access first published online on January 22, 2004
This version published online on February 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/btg429
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received November 6, 2002
Revised April 23, 2003
Accepted July 22, 2003

Article

Rapid and sensitive dot-matrix methods for genome analysis

Yue Huang 1* Ling Zhang 1

1 Lynnon Corporation, 116 rue du Milicien, Vaudreuil-Dorion, Quebec, Canada, J7V 9M4

* To whom correspondence should be addressed. E-mail: yhuang{at}lynnon.com.


  Abstract

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 http://www.lynnon.com/dotplot/index.html.


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