Generate sequence alignment and heatmap for TF binding sites
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2.3 years ago
rioualen ▴ 610

Hi, I'm looking for programs to generate heatmaps from DNA sequences (TF binding sites) and clusterize them. I like this type of figure but it's from a Matlab library, and I haven't found equivalents in R or else. Any suggestions? Thanks a lot!

Figure

alignment ChIP-Seq logo heatmap • 1.2k views
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2.3 years ago
Asaf 8.9k

You've got good old WebLOGO. It doesn't produce the heatmap but honestly, I think it doesn't add any information.

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Yeah I know it, but I'm not looking to produce the logo, I'm rather interested in how the sequences possibly cluster into subgroups, or if they're more like a continuum.

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So you can represent the MSA as a matrix and you plain heatmap

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