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Bioinformatics Advance Access published online on March 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti377
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received September 26, 2004
Revised February 2, 2005
Accepted March 4, 2005

Applications note

SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)

Fengkai Zhang 1 and Zhongming Zhao 2*

1 Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
2 Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA; Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA 23284, USA; Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China

* To whom correspondence should be addressed.
Zhongming Zhao, E-mail: zzhao{at}vcu.edu


  Abstract

Summary: SNPNB is a user-friendly and platform-independent application for analyzing single nucleotide polymorphism neighboring sequence context and nucleotide bias patterns, and subsequently evaluating the effective SNP size for the bias patterns observed from the whole data. It was implemented by Java and Perl. SNPNB can efficiently handle genome-wide or chromosome-wide SNP data analysis in a PC or workstation. It provides visualizations of the bias patterns for SNPs or each type of SNPs.

Availability: SNPNB and its full description are freely available at http://bioinfo.vipbg.vcu.edu/SNPNB/.


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This article has been cited by other articles:


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SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W642 - W644.
[Abstract] [Full Text] [PDF]


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