# 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 ...
221 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 ...
158 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)\\ \...
61 views

### 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 ...
83 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 ...
77 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 ...
341 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 ...