Questions tagged [hidden-markov-models]

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HMM Profile from Convergence of retrotransposons in oomycetes and plants

I am trying to recreate the experiment from Convergence of retrotransposons in oomycetes and plants by Kirill Ustyantsev, Alexandr Blinov and Georgy Smyshlyaev. In the "Methods" section a HMM ...
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Generating sequences from HMM

I encountered this question in a textbook (source: https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.721.2540&rep=rep1&type=pdf) and was trying to workout the solution for it. Was ...
3
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1answer
93 views

How to use the hmmsearch on prototypic repetitive sequences Repbase Update database?

I want to use the hmmsearch proposed in Convergence of retrotransposons in oomycetes and plants by Kirill Ustyantsev, Alexandr Blinov and Georgy Smyshlyaev. After the help from terdon I managed to ...
1
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1answer
105 views

What does instantaneous rate matrix mean?

PhyML is a tool used for maximum likelihood estimation analysis. I was running a PhyML analysis to check the rate of nucleotide change in DNA sequences and in the PhyML output, there are rate ...