enoLOGOS: a versatile web tool for energy normalized sequence logos.
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/.
Workman
Christopher T
CT
Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. cworkman@bioeng.ucsd.edu
Yin
Yutong
Y
Corcoran
David L
DL
Ideker
Trey
T
Stormo
Gary D
GD
Benos
Panayiotis V
PV
D000596:Amino Acids / Q000737:chemistry; D001665:Binding Sites; D003196:Computer Graphics; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D020407:Internet; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface; D016335:Zinc Fingers
D000596:Amino Acids; D004268:DNA-Binding Proteins