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how to detect repetitive motifs in gene?

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

gene repetitive
• 2,233 views • link
updated by Antonio R. Franco Antonio R. Franco • written by agata88 agata88

Looking at dotplots may be surprisingly effective.

• 1 views • link
written by GenoMax GenoMax

3 answers

try RepeatMasker first

• 1 views • link
written by chen chen

Thanks, I'll try that first

• 1 views • link
written by agata88 agata88

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).

• 1 views • link
written by harold.smith.tarheel harold.smith.tarheel

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

• 1 views • link
written by Antonio R. Franco Antonio R. Franco

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