how to detect repetitive motifs in gene?

Question

[agata88]

Hi all,

Do you know a tool that can detect repetitive motifs in gene? Especially in amplicons from multiplex analysis.

I would appreciate for any suggestions,

Best,

Agata

[GenoMax]

Looking at dotplots may be surprisingly effective.

Answer 1

[chen]

try RepeatMasker first

[agata88]

Thanks, I'll try that first

Answer 2

[harold.smith.tarheel]

For perfect repeats, a kmer counter with sufficiently small k would work. For imperfect repeats, BLAST alignment of gene against itself can be useful (and dot matrix display provides a tool for visualizing the positions and numbers of repeats).

Answer 3

[Antonio R. Franco]

Look for Dotlet. It is one of the best dotplot programs available