Algorithms for path-constrained sequence alignment

DOI10.1016/J.JDA.2013.09.003MaRDI QIDQ396718zbMATH OpenOpenAlexWikidataFDO

Authors Tamar Pinhas, Nimrod Milo, Gregory Kucherov, Michal Ziv-Ukelson

Publication date 13 August 2014

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

Full work available at URL https://doi.org/10.1016/j.jda.2013.09.003

zbMATH Keywords

dynamic programmingmiRNAregular expressionssequence alignment

Mathematics Subject Classification ID

Formal languages and automata (68Q45) Algorithms on strings (68W32) Protein sequences, DNA sequences (92D20)

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Cites work

• Algorithms for path-constrained sequence alignment
• Algorithms on Strings, Trees and Sequences
• Biological Sequence Analysis
• Comparing the size of NFAs with and without \(\epsilon\)-transitions
• Fast Pattern Matching in Strings
• scientific article; zbMATH DE number 3471577 (Why is no real title available?)
• Regular expression constrained sequence alignment
• Regular language constrained sequence alignment revisited
• SA-REPC -- sequence alignment with regular expression path constraint
• Verifying candidate matches in sparse and wildcard matching

Cited in

(9)

• A polyhedral approach to sequence alignment problems
• An efficient algorithm for attribute-based subsequence matching
• Approximate regular expression pattern matching with concave gap penalties
• Constrained sequence alignment: A general model and the hardness results
• scientific article; zbMATH DE number 2086217 (Why is no real title available?)
• SA-REPC -- sequence alignment with regular expression path constraint
• Algorithms for path-constrained sequence alignment
• A path selection approach to global pairwise sequence alignment using integer linear optimization†
• Parametric sequence alignment with constraints

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