enoLOGOS: a versatile web tool for energy normalized sequence logos | Zendy

Christopher T. Workman | Zendy; Yutong Yin | Zendy; David L. Corcoran | Zendy; Trey Ideker | Zendy; Gary D. Stormo | Zendy; Panayiotis V. Benos | Zendy

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enoLOGOS: a versatile web tool for energy normalized sequence logos

Author(s) -

Christopher T. Workman,

Yutong Yin,

David L. Corcoran,

Trey Ideker,

Gary D. Stormo,

Panayiotis V. Benos

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki439

Subject(s) - logos bible software , biology , sequence alignment , web server , sequence (biology) , set (abstract data type) , sequence logo , sequence motif , energy (signal processing) , computational biology , computer science , peptide sequence , genetics , dna , world wide web , mathematics , the internet , gene , programming language , statistics , operating system

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/.

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