#5564. Fast parallel construction of variable-length Markov chains

August 2026publication date
Proposal available till 21-05-2025
4 total number of authors per manuscript0 $

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Journal’s subject area:
Applied Mathematics;
Computer Science Applications;
Biochemistry;
Structural Biology;
Molecular Biology;
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Abstract:
Background: Alignment-free methods are a popular approach for comparing biological sequences, including complete genomes. The methods range from probability distributions of sequence composition to first and higher-order Markov chains, where a k-th order Markov chain over DNA has 4 k formal parameters. To circumvent this exponential growth in parameters, variable-length Markov chains (VLMCs) have gained popularity for applications in molecular biology and other areas. VLMCs adapt the depth depending on sequence context and thus curtail excesses in the number of parameters. The scarcity of available fast, or even parallel software tools, prompted the development of a parallel implementation using lazy suffix trees and a hash-based alternative.
Keywords:
Alignment-free; Parallel algorithms; Sequence analysis; Variable-length Markov chain

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