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Sequence logo generation software tools | High-throughput sequencing data analysis

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.

Source text:
(Workman et al., 2005) enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res.

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kpLogo / k-mer probability logo
Integrates detection and visualization of position-specific ultra-short motifs within macromolecules. kpLogo overcomes the limitations of conventional motif-visualization tools in handling positional interdependencies and utilizing ranked or weighted sequences increasingly available from high-throughput assays. It generates a new type of logo plot called the k-mer logo, in which at each position the most significant k-mer is plotted vertically with the total height scaled to its P value or test statistics, as appropriate. kpLogo can be accessed at a simple webserver which generates frequency, information-content, and probability logos in addition to k-mer logos. Its source code is freely available.
Gene Slider
Helps visualize the conservation and entropy of orthologous DNA and protein sequences by presenting them as one long sequence logo that can be zoomed in and out of, from an overview of the entire sequence down to just a few residues at a time. A search function enables users to find motifs such as cis-elements in promoter regions by simply ‘drawing’ a sequence logo representation of the desired motif as a query. Gene Slider combines the ability to make long sequence logos with a search panel that automatically highlights motifs of interest, even when there is a high degree of wobble.
Provides an intuitive visualization of motif differences. DiffLogo is an easy-to-use tool for a fast and efficient comparison of motifs. It may be applied by users with only basic knowledge in R and is highly configurable and extensible for advanced users. It enables the illustration and investigation of differences between highly similar motifs such as binding patterns of transcription factors for different cell types, treatments, and algorithmic approaches. Using DiffLogo, it is easily possible to compare motifs from different sources, so DiffLogo facilitates decision making, knowledge sharing, and the presentation of results.
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