Long tandem repeat motif comparison

[dabitz]

Hi Martin,
Is difflogo able to compare more than two long tandem repeat motifs? I am working on the evolution of a specific family of centromeric tandem repeats across several species and the motifs (sequence logos) have a lenght of around 170 positions. Although I was able to compare two motifs, the webserver is crushing when I try with three or more motifs...
Best,
André

[mgledi]

Hey Andre,
You are right that DiffLogo has problems with this large motifs.

1. You can try the R-package instead of the WebServer.
2. We can workaround your problem. I don't think that anybody can recognize something from 170 motif positions. For only one DiffLogo this means 170 x 4 x 2 Symbols to digest visually.

[dabitz]

Since the tandem repeat I am working on it has shown strong phylogenetic signal, thus, I am interested to build a motif-based clustering of the sequence logos to check whether I get good evolutionary groups. Not sure if I will be able to do it with DiffLogo...

[mgledi]

Hey Andre,

I think DiffLogo is not the best tool for your problem. You should give motifStack a try.