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Bioinformatics Advance Access originally published online on April 21, 2006
Bioinformatics 2006 22(12):1536-1537; doi:10.1093/bioinformatics/btl151
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments

Vladimir Vacic 1, Lilia M. Iakoucheva 2 and Predrag Radivojac 3,*

1 Computer Science and Engineering Department, University of California Riverside, CA, USA
2 Laboratory of Statistical Genetics, The Rockefeller University New York, NY, USA
3 School of Informatics, Indiana University Bloomington, IN, USA

*To whom correspondence should be addressed at School of Informatics, Indiana University, 1900 East 10th Street, Eigenmann Hall 1005, Bloomington, IN 47406, USA

Sumary: Two Sample Logo is a web-based tool that detects and displays statistically significant differences in position-specific symbol compositions between two sets of multiple sequence alignments. In a typical scenario, two groups of aligned sequences will share a common motif but will differ in their functional annotation. The inclusion of the background alignment provides an appropriate underlying amino acid or nucleotide distribution and addresses intersite symbol correlations. In addition, the difference detection process is sensitive to the sizes of the aligned groups. Two Sample Logo extends WebLogo, a widely-used sequence logo generator. The source code is distributed under the MIT Open Source license agreement and is available for download free of charge.

Availability: http://www.twosamplelogo.org

Contact: predrag{at}indiana.edu

Received on December 29, 2005; revised on March 19, 2006; accepted on April 14, 2006

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