Questions tagged [bioinformatics]

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Sequence Alignment with Skips

In my thesis I am working on a problem connected with sequence alignment, in particular, I deal with the Dynamic Time Warping (DTW) algorithm (see this for more), which is used to evaluate the ...
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0answers
240 views

Sequence Alignment with general gap penalties: proof of optimal substructure

I am very well-aware of how optimal substructure for pairwise global sequence alignment using the Needleman-Wunsch algorithm works. However, I have merely seen hand-waving explanations for the ...
1
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0answers
242 views

Waterman-Smith-Beyer Algorithm

I am having trouble understanding the affine gap penalty in the following example - Waterman-Smith-Beyer Algorithm: \begin{align*} D_{0,0} &= 0\\ D_{0,j} &= g(j)\\ D_{i,0} &= g(i)\\ \...
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a variant of Fitch's algorithm when it is known that one path has cost 0?

Fitch's algorithm solves the small parsimony problem - given tree topology and leaf labels, but not internal node labels, find best internal node labels (i.e. best score) for that tree. The score is ...
1
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0answers
125 views

proving that local sequence alignment can be done in linear space

according to the Smith-Waterman setup, I have 2 string sequences S and T, and I want to identify their respective subsequences $\alpha$ and $\beta$ whose global alignment have maximum score over all ...
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0answers
82 views

Multiple sequence Progressive alignment example using five sequences

I tried to find sources that explain multiple sequence alignment with an example using progressive alignment, but I couldn't find one. I actually know till creating a guide tree, after creating a ...
0
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0answers
26 views

data structures/ Classes for RNA & DNA

In bioinformatics they study biological data. I have seen codes dealing with DNA sequences. However, they are treated as string literal. I was wondering if there were data structures or classes in OOP ...
0
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1answer
451 views

multiple sequence alignment using HMM and simulated annealing

Can anyone help me with Multiple Sequence Alignment (MSA) using Hidden Markov Model (HMM) by giving an example or a reference except these 2 references: 1-Eddy, Sea.R., et al.Multiple alignment using ...
0
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0answers
61 views

Graph theoretical approach to compare n pair of variables along a set of interval

I am dealing a bioinformatics problem and need help in approaching it in the right direction. I have a set of variables that represent different kinds of genomic data and are real valued. I am trying ...
0
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0answers
26 views

Are there any algorithms or researches on finding local alignments in partially ordered sequences?

The question is a bit unclear, so let me explain. Finding local alignments in sequences like protein sequence is a well studied area in bioinformatics, and I do not think there is any lack of ...