Shuffling biological sequences

DOI10.1016/S0166-218X(97)81456-4MaRDI QIDQ5961624zbMATH OpenOpenAlexFDO

Authors D. Kandel, Y. Matias, R. Unger, Peter Winkler

Publication date 4 November 1997

Published in Discrete Applied Mathematics (Search for Journal in Brave)

Full work available at URL http://www.elsevier.com/locate/dam

zbMATH Keywords

amino acidsbiological sequencesdinucleotidesdoubletsEuler toursmolecular biologypermutationssequence shuffling algorithmstriplets

Mathematics Subject Classification ID

Applications of graph theory (05C90) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

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Cites work

• Approximate string-matching with q-grams and maximal matches
• DNA physical mapping and alternating Eulerian cycles in colored graphs
• scientific article; zbMATH DE number 3138903 (Why is no real title available?)
• scientific article; zbMATH DE number 3934150 (Why is no real title available?)
• scientific article; zbMATH DE number 3688740 (Why is no real title available?)
• Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.
• The Random Walk Construction of Uniform Spanning Trees and Uniform Labelled Trees
• Trailing the dovetail shuffle to its lair

Cited in

(11)

• Euler circuits and DNA sequencing by hybridization
• Random walks on a finite graph with congestion points
• Constrained Markov order surrogates
• Exact goodness-of-fit tests for Markov chains
• How to couple from the past using a read-once source of randomness
• Exact distribution of word counts in shuffled sequences
• Testing homogeneity in dynamic discrete games in finite samples
• Las Vegas algorithms to generate universal cycles and de Bruijn sequences uniformly at random
• Finite automata for testing composition-based reconstructibility of sequences
• Shuffling biological sequences with motif constraints
• Revisiting the relationship between compositional sequence complexity and periodicity

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