Question: how to detect repetitive motifs in gene?
1
gravatar for agata88
3.1 years ago by
agata88790
Poland
agata88790 wrote:

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

repetitive gene • 853 views
ADD COMMENTlink modified 3.1 years ago by Antonio R. Franco4.0k • written 3.1 years ago by agata88790
1

Looking at dotplots may be surprisingly effective.

ADD REPLYlink written 3.1 years ago by genomax68k
0
gravatar for chen
3.1 years ago by
chen1.9k
OpenGene
chen1.9k wrote:

try RepeatMasker first

ADD COMMENTlink written 3.1 years ago by chen1.9k

Thanks, I'll try that first

ADD REPLYlink written 3.1 years ago by agata88790
0
gravatar for harold.smith.tarheel
3.1 years ago by
United States
harold.smith.tarheel4.4k wrote:

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).

ADD COMMENTlink written 3.1 years ago by harold.smith.tarheel4.4k
0
gravatar for Antonio R. Franco
3.1 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

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

ADD COMMENTlink written 3.1 years ago by Antonio R. Franco4.0k
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