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Bioinformatics Advance Access originally published online on August 4, 2008
Bioinformatics 2008 24(19):2254-2255; doi:10.1093/bioinformatics/btn407
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BLogo: a tool for visualization of bias in biological sequences

Wencheng Li 1,{dagger}, Bo Yang 1,{dagger}, Shaoguang Liang 2, Yonghua Wang 3, Chris Whiteley 4, Yicheng Cao 1 and Xiaoning Wang 1,*

1School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510641, 2National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, 3College of Light Industry and Food Sciences, Key Lab of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510641, China and 4Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown 6139, South Africa

*To whom correspondence should be addressed.


  Abstract

Summary: Blogo is a web-based tool that detects and displays statistically significant position-specific sequence bias with reduced background noise. The over-represented and under-represented symbols in a particular position are shown above and below the zero line. When the sequences are in open reading frames, the background frequency of nucleotides could be calculated separately for the three positions of a codon, thus greatly reducing the background noise. The {chi}2-test or Fisher's exact test is used to evaluate the statistical significance of every symbol in every position and only those that are significant are highlighted in the resulting logo. The perl source code of the program is freely available and can be run locally.

Availability: http://acephpx.cropdb.org/blogo/, http://www.bioinformatics.org/blogo/

Contact: lwcbio{at}yahoo.com.cn; xnwang{at}21cn.net

Supplementary information: Supplementary data are available atBioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors are regarded as joint First Authors.

Associate Editor: Limsoon Wong

Received on May 21, 2008; revised on July 10, 2008; accepted on July 29, 2008

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