Questions tagged [hidden-markov-models]

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Profile HMM to find sequence motif using Baum-Welch instead of using a given multiple sequence alignment?

I know this can be very problem-specific -- but it seemed to me the standard approach to train an HMM to recognize a binding pattern of a protein is to use the multiple sequence alignment (MSA), ...
6
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2answers
242 views

Sequence alignment using Markov Model

I am learning about applying Markov model to sequence alignment. The prof says that the transition probabilities from a gap-residue alignment to a residue-gap alignment and vice versa are both 0. Is ...
5
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1answer
98 views

How to convert the given mathematical computation (on biological problem) to mathematical fomula, equation?

I have crossposted this question in maths StackExchange. The problem is dominantly mathematical (this question) but the application of the problem is mainly biological. Hoping that people in this ...
5
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1answer
125 views

What is the meaning of the Hmmer profile?

I want to understand what the hmmer Profile used in hmmer. consider the profile ...
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0answers
42 views

How to rebuild the workflow for mining in oomynete genomes in UGENE

I want to recreate the UGENE workflow proposed in Convergence of retrotransposons in oomycetes and plants. After being able to understand the data and hmmsearch Here and Here and getting most of the ...
3
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1answer
60 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 ...
4
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1answer
98 views

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 ...
2
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2answers
232 views

Why PHMM is used For Protein Analysis

I am interested on how profile hidden markov model is used for protein analysis in bioinformatics. Can you guys explain why phmm is more preferable method comparing to simple MSA(Multiple Sequence ...
12
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3answers
188 views

Generic HMM solvers in bioinformatics?

Hidden Markov models (HMMs) are used extensively in bioinformatics, and have been adapted for gene prediction, protein family classification, and a variety of other problems. Indeed, the treatise by ...