TY - JOUR
T1 - enoLOGOS
T2 - A versatile web tool for energy normalized sequence logos
AU - Workman, Christopher T.
AU - Yin, Yutong
AU - Corcoran, David L.
AU - Ideker, Trey
AU - Stormo, Gary D.
AU - Benos, Panayiotis V.
N1 - Funding Information:
The authors would like to thank Claus A. Andersen for sharing code from his logo program. This work was supported by NSF grant MCB0316255. T.I. is funded by NCRR 018627. C.T.W. is funded by NIH 5T32HL07089-30. Funding to pay the Open Access publication charges for this article was provided by NSF grant MCB0316255.
PY - 2005/7
Y1 - 2005/7
N2 - 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/.
AB - 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/.
UR - http://www.scopus.com/inward/record.url?scp=22344457014&partnerID=8YFLogxK
U2 - 10.1093/nar/gki439
DO - 10.1093/nar/gki439
M3 - Article
C2 - 15980495
AN - SCOPUS:22344457014
SN - 0305-1048
VL - 33
SP - W389-W392
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 2
ER -