enoLOGOS: a versatile web tool for energy normalized sequence logos - PubMed (original) (raw)
enoLOGOS: a versatile web tool for energy normalized sequence logos
Christopher T Workman et al. Nucleic Acids Res. 2005.
Abstract
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/.
Figures
Figure 1
Examples of input weight matrices (horizontal and vertical).
Figure 2
Example of C2H2-enoLOGOS and enoLOGOS output. In this example, the _x_-axis of the C2H2-enoLOGOS output (top) represents the ‘contacting’ amino acid positions of fingers 3, 2 and 1, respectively. The output of web tool enoLOGOS (bottom) contains a grey-scale-coded matrix plot of the mutual information of each pair of positions of the alignment.
References
- Schneider T.D., Stormo G.D., Gold L., Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 1986;188:415–431. - PubMed
- Bulyk M.L., Gentalen E., Lockhart D.J., Church G.M. Quantifying DNA–protein interactions by double-stranded DNA arrays. Nat. Biotechnol. 1999;17:573–577. - PubMed
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- 018627/PHS HHS/United States
- T32 HL007089/HL/NHLBI NIH HHS/United States
- 5T32HL07089-30/HL/NHLBI NIH HHS/United States
- P41 RR018627-030005/RR/NCRR NIH HHS/United States
- P41 RR018627-048666/RR/NCRR NIH HHS/United States
- P41 RR018627-055039/RR/NCRR NIH HHS/United States
- P41 RR018627-048686/RR/NCRR NIH HHS/United States
- P41 RR018627-020005/RR/NCRR NIH HHS/United States
- P41 RR018627-055059/RR/NCRR NIH HHS/United States
- P41 RR018627/RR/NCRR NIH HHS/United States