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

Fengkai Zhang; Zhongming Zhao

doi:10.1093/bioinformatics/bti377

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

Bioinformatics. 2005 May 15;21(10):2517-9. doi: 10.1093/bioinformatics/bti377. Epub 2005 Mar 15.

Authors

Fengkai Zhang¹, Zhongming Zhao

Affiliation

¹ Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA.

PMID: 15769840
DOI: 10.1093/bioinformatics/bti377

Abstract

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/

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Base Pair Mismatch / genetics*
Base Sequence
Chromosome Mapping / methods*
Computer Graphics
Genome, Human
Humans
Molecular Sequence Data
Nucleotides / genetics*
Polymorphism, Single Nucleotide / genetics*
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Software
User-Computer Interface*

Substances

Nucleotides