Question: kmer analysis for sequences of behavior
gravatar for truebeliever24
12 weeks ago by
truebeliever2420 wrote:

Hi all,

I have been trying to use kmer analysis (using k=3) to identify phenotypes of behavioral sequences.

For example, if each letter is a behavior within a courtship display, I could have the following:

Species A: R R R R R S H E
Species B: P P P P P P A S H E
Hybrid 1: P P P P R R E
Hybrid 2: R R R R R P E

The idea is for the kmer to be able to separate all individuals into species A, B, and various hybrid phenotypes based on the sequences they perform. It has actually done a very good job separating the parent species and intermediate hybrids, but seemingly backcrossed hybrids (i.e., act like Species A, but do a single behavior that Species B does) are often placed incorrectly with Species A).

I've tried to find ways to weigh characters or eliminate repetitive 3mers to try and avoid biasing the analysis, but I haven't been able to do so.

Is anyone familiar with kmer analysis? If so, do you have any suggestions?

R • 141 views
ADD COMMENTlink modified 12 weeks ago by zx87548.2k • written 12 weeks ago by truebeliever2420

Looks like a problem for a hidden Markov model.

ADD REPLYlink written 12 weeks ago by Michael Dondrup46k
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