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Bioinformatics Advance Access originally published online on March 15, 2005
Bioinformatics 2005 21(10):2517-2519; 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{at}oupjournals.org

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

Fengkai Zhang 1 and Zhongming Zhao 1,2,3,*

1Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University Richmond, VA 23298, USA
2Center for the Study of Biological Complexity, Virginia Commonwealth University Richmond, VA 23284, USA
3Kunming Institute of Zoology, Chinese Academy of Sciences Kunming, Yunnan 650223, China

*To whom correspondence should be addressed at: Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, PO Box 980126, Richmond, VA 23298-0126, USA

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 a 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/

Contact: zzhao{at}vcu.edu


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Home page
 Nucleic Acids ResHome page
A. Han, H. J. Kang, Y. Cho, S. Lee, Y. J. Kim, and S. Gong
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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