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Questions tagged [bioinformatics]

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2 votes
1 answer
90 views

Proof of dynamic programming calculation of Levenshtein distance

Let s1 and s2 are 2 arbitrary strings with lengths l1 and ...
St.Antario's user avatar
0 votes
0 answers
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 ...
Enforce's user avatar
  • 181
3 votes
1 answer
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 $d_0 = H(s_1,s_2)$....
Harry L's user avatar
  • 31
1 vote
0 answers
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 ...
Mowgli's user avatar
  • 111
3 votes
1 answer
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 ...
ilia's user avatar
  • 153
6 votes
2 answers
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 ...
Hans-Peter Stricker's user avatar
5 votes
2 answers
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,...
Distance's user avatar
4 votes
2 answers
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 ...
Dr Fabio Gori's user avatar
0 votes
1 answer
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 ...
Douglas S. Stones's user avatar
1 vote
1 answer
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 $\binom{n}{k}$...
Christoph's user avatar
3 votes
1 answer
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 ...
Tianyang Li's user avatar
8 votes
3 answers
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 ...
Lisa's user avatar
  • 83
4 votes
3 answers
2k views

Correspondence between Viterbi algorithm and Smith-Waterman

Viterbi is an algorithm for finding the maximum likelihood assignment to the hidden variables of an HMM, given the observed variables (we know the transition and emission probabilities of the HMM). ...
Jonathan's user avatar
  • 233