# Questions tagged [bioinformatics]

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### Proof of dynamic programming calculation of Levenshtein distance

Let s1 and s2 are 2 arbitrary strings with lengths l1 and ...
• 203
67 views

### Texts on coalescent theory/probability methods for DNA evolution

I am starting a PhD on mitochondrial evolution modelling with a focus on probabilistic methods and coalescent theory. For this purpose, I am looking for advanced textbooks on probability methods for ...
• 181
180 views

### Distribution of the change in Hamming distance between two sequences

Suppose I have two strings $s_1$ and $s_2$ of equal length $L$ with an alphabet size of $k \geq 2$. Suppose further that these two strings initially have a Hamming distance equal to $d_0 = H(s_1,s_2)$....
• 31
1 vote
41 views

### Mathematical modeling of multi-site reaction-diffusion

(I asked a similar question on Mathematics SE, but based on the Help section it might be better suited for this site, as it is focused on research-level mathematical modeling.) I am wondering if ...
• 111
193 views

### Matching two sequences between each other

Given the sequence of symbols $A$ (contains ~10,000 symbols) and sequence of blocks $B$ (contains ~3,000 blocks, ~30 symbols inside each block) I need to exclude some blocks from sequence $B$ so that ...
• 153
858 views

### Human brains considered as directed graphs

I assume that human brains can be considered as directed graphs with neurons as nodes and synapses as edges. I explicitly don't want to consider the weights, the dynamics of neural activity (based on ...
• 9,642
541 views

### Neighbourhood of a word and Levenshtein distance

The Levenshtein distance or Edit distance $$lev(U,V)$$ between two strings $U$ and $V$ over a finite alphabet $\Sigma$ of size $\left| \Sigma \right| = \sigma ,$ is the minimal number of insertions,...
• 61
1k views

### Industry jobs involving mathematics, machine learning and biology [closed]

I have a MSc in Mathematics and a PhD in Bioinformatics (in two different European countries); during the PhD I was developing computational methods to analyse DNA sequence data, mainly using a ...
158 views

### Generating spatially-aware degree-preserving random graphs?

In the study of biological neural networks, researchers sometimes compare hypotheses vs. a degree-preserving random null model. One major criticism against this approach is that connections in neural ...
• 4,229
1 vote
333 views

### Maximal difference between k randomly drawn numbers from 1 to n – Looking for formula to sequence

Hello! I have an interesting problem that seemed simple to me, but I'm unable to solve it on my own. Suppose I am drawing k numbers out of n numbers labeled from 1 to n. Considering all $\binom{n}{k}$...
523 views

### Cover a line segment randomly with smaller line segments

Covering a circle randomly with arcs has been well studied in the past (Geometric Probability - Solomon). But the problem when the circle is changed to a line segment doesn't seem to have been ...
• 161
507 views

### MicroArray, tesing if a sample is the same with high variance data.

I'll explain the problem but what I am looking for is a few suggested methods to approach this problem. You don't need to know what a microarray but if you are interested look here link text The info ...
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