7
votes
Accepted
Generic HMM solvers in bioinformatics?
I would also recommend to take a look at pomegranate, a nice Python package for probabilistic graphical models. It includes solvers for HMMs and much more. Under the hood it uses Cythonised code, so ...
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6
votes
Accepted
Sequence alignment using Markov Model
If I understand your question correctly, then I think for case of pairwise alignment, there is a simple explanation.
I believe the key insight is that: a mismatch should always score better than a ...
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5
votes
Generic HMM solvers in bioinformatics?
There are certainly software libraries for working with HMMs. For a general-purpose implementation in C++, take a look at the SeqAn HMM algorithms.
For your purposes, i.e. “computing … the most ...
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4
votes
Generic HMM solvers in bioinformatics?
If I remember correctly Ewan Birney's Dynamite (a compiler-compiler) as presented at ISMB 1997 had this functionality, there is also some code here on GitHub https://github.com/birney/wise3 which at ...
- 1,069
2
votes
Accepted
HMM Profile from Convergence of retrotransposons in oomycetes and plants
The alignment they used to build the HMM is included as supplementary file 8 in the paper you cite:
Multiple amino acid sequence alignment of RNH genes and domains from diverse taxa constructed and ...
- 10.6k
2
votes
probability of an entire sequence, not just one value
The author writes in the quote that $O$ is to be taken for the whole set of positions $O_{i}$.
In the extracts that you provide there is no reason to believe that it is only for a sequence of length 1....
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2
votes
request for peer reviewed articles using Markov Chains
There are very many examples of Markov chains in the life sciences. They are foundational models for many applications:
dynamic programming (sequence alignment)
Hidden Markov Models (genomic ...
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1
vote
Accepted
Generating sequences from HMM
[Comments from other post migrated as answer]
The parenthetical statement in the first bullet point says without corrections. In which case, if an unseen nucleotide has a probability of zero, the ...
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1
vote
Accepted
What does instantaneous rate matrix mean?
Reversible At its simplist the GTR rate, is the General Time Reversible model and most importantly infers the matrix is "reversible", thus as many A mutations will go to C as C mutations go ...
M__♦
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1
vote
Sequence alignment using Markov Model
All Chris_Rands said is correct: you set the probability of $X\to Y$ and $Y\to X$ to 0 to forbid adjacent insertions/deletions in the alignment. A lot of textbooks including some classical ones use ...
- 6,605
1
vote
How to convert the given mathematical computation (on biological problem) to mathematical fomula, equation?
I am not sure I understood all, but what you do is like doing a Markov chain but instead of saying that the previous position(s) decides the fate of the next one(s) is the block what determines which ...
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1
vote
Accepted
What is the meaning of the Hmmer profile?
The tutorial in the documentation does indeed state what you quoted but a full description of the file format is given in Section 8 of the documentation, starting on page 106.
To summarise, as you ...
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1
vote
Accepted
How to use the hmmsearch on prototypic repetitive sequences Repbase Update database?
RepBase explain what these files are on their website. It is usually a good idea to check the documentation when downloading files so you know what you're downloading.
Based on the list of files ...
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1
vote
Why PHMM is used For Protein Analysis
The simple probabilistic scoring scheme you describe to query a target sequence against a (protein) family represented as a multiple sequence alignment (MSA) is actually similar in essence to a ...
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