Fast parallel construction of variable-length Markov chains

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 paramete...

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Bibliographic Details
Published in:	BMC bioinformatics Vol. 22; no. 1; pp. 1 - 23
Main Authors:	Gustafsson, Joel, Norberg, Peter, Qvick-Wester, Jan R., Schliep, Alexander
Format:	Journal Article
Language:	English
Published:	London BioMed Central 09.10.2021 BioMed Central Ltd Springer Nature B.V BMC
Subjects:	Algorithms alignment Alignment-free Bayesian analysis Biochemistry & Molecular Biology Bioinformatics Bioinformatics (Computational Biology) Bioinformatik (beräkningsbiologi) Biomedical and Life Sciences Biotechnology & Applied Microbiology Children & youth Computational Biology/Bioinformatics Computer Appl. in Life Sciences Distribution (Probability theory) Dynamic programming Freeware Gene sequencing Genomes Genomics Life Sciences Machine learning Markov analysis Markov chains Markov processes Mathematical & Computational Biology Methods Microarrays Molecular biology Novel computational methods for analysis of biological systems Parallel algorithms Parallel programming (Computer science) Parameters Portable computers prediction probabilistic-automata Sequence analysis Software Software development tools Source code Suffix trees Variable-length Markov chain Sweden Variable-length Markov chain Alignment-free Sequence analysis Parallel algorithms
ISSN:	1471-2105, 1471-2105
Online Access:	Get full text
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