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Nucleic Acids Research 2005 33(Web Server Issue):W389-W392; doi:10.1093/nar/gki439
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

enoLOGOS: a versatile web tool for energy normalized sequence logos

Christopher T. Workman*, Yutong Yin1,2, David L. Corcoran3,4, Trey Ideker, Gary D. Stormo5 and Panayiotis V. Benos1,2,3

Department of Bioengineering, University of California at San Diego 9500 Gilman Drive, La Jolla, CA 92093, USA 1Department of Computational Biology, University of Pittsburgh Pittsburgh, PA 15261, USA 2University of Pittsburgh Cancer Institute, School of Medicine, University of Pittsburgh Pittsburgh, PA 15261, USA 3Department of Human Genetics, University of Pittsburgh Pittsburgh, PA 15261, USA 4Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh Pittsburgh, PA 15261, USA 5Department of Genetics, School of Medicine, Washington University in St Louis MO, USA

*To whom correspondence should be addressed. Email: cworkman{at}bioeng.ucsd.edu

Received February 14, 2005. Revised March 28, 2005. Accepted March 28, 2005.

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position. Currently, the available web servers are able to create logo images from a set of aligned sequences, but none of them generates weighted sequence logos directly from energy measurements or other sources. With the advent of high-throughput technologies for estimating the contact energy of different DNA sequences, tools that can create logos directly from binding affinity data are useful to researchers. enoLOGOS generates sequence logos from a variety of input data, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence, a unique feature of this tool. Another web interface for our software, C2H2-enoLOGOS, generates logos for the DNA-binding preferences of the C2H2 zinc-finger transcription factor family members. enoLOGOS and C2H2-enoLOGOS are accessible over the web at http://biodev.hgen.pitt.edu/enologos/.

Correspondence may also be addressed to Gary D. Stormo. Email: stormo{at}genetics.wustl.edu or Panayiotis V. Benos at A300 Crabtree Hall, Department of Human Genetics, GSPH, 130 DeSoto Street, Pittsburgh, PA 15261, USA. Tel: +1 412 648 3315; Fax: +1 412 624 3020; Email: benos{at}pitt.edu


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