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/.

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Figures

Figure 1

Figure 1

Examples of input weight matrices (horizontal and vertical).

Figure 2

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.

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