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Bioinformatics Advance Access published online on October 20, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn547
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Effective Cluster-Based Seed Design for Cross-Species Sequence Comparisons

Leming Zhou a,*, Ingrid Mihai a and Liliana Florea a,*

aDepartment of Computer Science, George Washington University, Washington DC 20052

*To whom correspondence should be addressed. Leming Zhou, E-mail: lmzhou{at}gwu.edu

*To whom correspondence should be addressed. Prof Liliana Florea, E-mail: florea{at}gwu.edu


  Abstract

Summary: To annotate newly sequenced organisms, cross-species sequence comparison algorithms can be applied to align gene sequences to the genome of a related species. To improve the accuracy of alignment, spaced seeds must be optimized for each comparison. As the number and diversity of genomes increases, an efficient alternative is to cluster pairwise comparisons into groups and identify seeds for groups instead of individual comparisons. Here we investigate a measure of comparison closeness and identify classes of comparisons that show similar seed behavior and therefore can employ the same seed.

Availability: Source code is freely available at http://dna.cs.gwu.edu and from Bioinformatics Online.

Contact: lmzhou{at}gwu.edu, florea{at}gwu.edu

Supplementary information: http://dna.cs.gwu.edu and Bioinformatics Online.

Associate Editor: Prof. John Quackenbush

Received on August 5, 2008; revised on October 10, 2008; accepted on October 17, 2008

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This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
L. Zhou, M. Pertea, A. L. Delcher, and L. Florea
Sim4cc: a cross-species spliced alignment program
Nucleic Acids Res., June 1, 2009; 37(11): e80 - e80.
[Abstract] [Full Text] [PDF]


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