Generate sequence alignment and heatmap for TF binding sites

Question

[rioualen]

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!

Answer 1

[Asaf]

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

[rioualen]

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.

[Asaf]

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