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Questions tagged [bioinformatics]

Algorithms, data-structures, and other theoretical questions arising from arising from bioinformatics

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Can information, eg. Shannon Entropy, be considered an absolute value?

This question is a distillation of my question here: How do I calculate the information content of a mass spectrum? Using a theoretical instrument that makes perfect measurements of fundamental ...
Ninja Chris's user avatar
5 votes
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Reconstruction of a sequence generated by a Markov chain - reference request

Let S be a finite sequence of symbols from a finite alphabet, with gaps - that is on some known locations an unknown number of symbols are missing. Assuming that the sequence , including the symbols ...
Popescu Claudiu's user avatar
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Applications of Combinatorial Games in Computational Biology

I'm looking for general references in the literature about applications of games algorithmics in computational biology. Q1. What are the notable cases of computational-biology or bioinformatics ...
XORwell's user avatar
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11 votes
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What paradigm of automated theorem proving is appropriate for Principia Mathematica-style formalization?

I am in possession of a book, which, inspired by Russell's Principia Mathematica (PM) and logical positivism, attempts to formalize a specific domain by determining axioms and deducing theorems from ...
Atriya's user avatar
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8 votes
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How hard is the origin of life problem?

The origin of life problem is the wide-ranging inquiry into the mechanisms underpinning the emergence of life, where one definition of life is "a self-sustained chemical system capable of undergoing ...
Jim G's user avatar
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4 votes
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an efficient algorithm for mismatch profile

We have M=10000 binary sequences of length N=1000. given length L=15, for each pair of sequences, $S_1$ and $S_2$, we define the mismatch profile, mp($S_1$,$S_2$,$L$)[$m$], for m=0,1,...,L as ...
mghandi's user avatar
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5 votes
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a data structure for partial sequences

We have a set of bit sequences of length $L$ with only $K$ known bits and $L-K$ gaps. We want to store them in a data structure in a way that given a new bit sequence $x$ of length $L$, with $L$ known ...
mghandi's user avatar
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8 votes
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Applications of computer science in biology

Is there a survey or tutorial article which talks about application of theoretical computer science to emerging fields of applications of computer science in biology, bioinformatics and nanotechnology?...