Shuffling biological sequences with motif constraints

DOI10.1016/j.jda.2007.06.001zbMath1145.92314OpenAlexW2026686302MaRDI QIDQ935837

Romain Rivière, Johanne Cohen, Alain Denise, Dominique Barith

Publication date: 8 August 2008

Published in: Journal of Discrete Algorithms (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jda.2007.06.001

zbMATH Keywords

NP-completenessrandom sequence generation

Mathematics Subject Classification ID

Analysis of algorithms and problem complexity (68Q25) Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08)

Uses Software

• PSI-BLAST
• BLAST

Cites Work

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• A unified approach to word occurrence probabilities
• Motif statistics.
• The Random Walk Construction of Uniform Spanning Trees and Uniform Labelled Trees
• On graphs with polynomially solvable maximum-weight clique problem
• How to Get a Perfectly Random Sample from a Generic Markov Chain and Generate a Random Spanning Tree of a Directed Graph
• Assessing the Statistical Significance of Overrepresented Oligonucleotides
• Shuffling biological sequences