Journal Article

BLogo: a tool for visualization of bias in biological sequences

Wencheng Li, Bo Yang, Shaoguang Liang, Yonghua Wang, Chris Whiteley, Yicheng Cao and Xiaoning Wang

in Bioinformatics

Volume 24, issue 19, pages 2254-2255
Published in print October 2008 | ISSN: 1367-4803
Published online June 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn407
BLogo: a tool for visualization of bias in biological sequences

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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 χ2-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@yahoo.com.cn; xnwang@21cn.net

Supplementary information: Supplementary data are available atBioinformatics online.

Journal Article.  925 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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