Questions tagged [hidden-markov-models]

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Available Protein sequence alignment dataset and HMM model

It may better to move the question here. I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to ...
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what is the difference between generalized profiles and pHMMs?

I am studying about Patterns,Profiles and HMMs. Can someone help me understand the difference between generalized profiles and pHMMs? Is there any good book/paper explaining in a clear/simple way ...
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phmm visualization

I have used HMMER search and I have created a phmm. But I would like to visualize it, not as a logo but as a phmm. I do not have Linux, so I cannot use build hmmer. Is there any web browser that I ...
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phmm blast hmmer

i have created a phmm in hmmer from a multiple alignment produced in tcoffee from sequences taken from blast similar to my query sequence. So I would like to ask how i can compare the results from ...
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0answers
24 views

What exactly does each of InterPro, PANTHER, Pfam bring to the table individually in classifying a protein?

I would be very grateful if somebody could sketch out the methods Pfam and PANTHER use to assign a family to a given protein and how they are different. My (cursory) understanding is that InterpProp ...
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19 views

probability of an entire sequence, not just one value

I am reading "Statistical methods in bioinformatics" I came across this formula: As explained in the book O are the observations: My question is why the author ...
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0answers
38 views

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), ...
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2answers
258 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 ...
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1answer
104 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
141 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
46 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 ...
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1answer
71 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 ...
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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 ...
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2answers
261 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 ...
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3answers
218 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 ...