Practical regular expression constrained sequence alignment

DOI10.1016/J.TCS.2020.02.017MaRDI QIDQ2310751zbMATH OpenOpenAlexFDO

Authors Lise Rommel Romero Navarrete, Guilherme P. Telles

Publication date 6 April 2020

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2020.02.017

zbMATH Keywords

finite automatonregular expressionconstrained sequence alignmentPROSITE

Mathematics Subject Classification ID

Formal languages and automata (68Q45) Algorithms on strings (68W32)

Recommendations

• Regular expression constrained sequence alignment
• Efficient algorithms for regular expression constrained sequence alignment
• Efficient Algorithms for Regular Expression Constrained Sequence Alignment
• Combinatorial Pattern Matching
• Regular language constrained sequence alignment revisited

Cites work

• scientific article; zbMATH DE number 3664335 (Why is no real title available?)
• A fast algorithm for the constrained multiple sequence alignment problem
• Combinatorial Pattern Matching
• Constrained sequence alignment: A general model and the hardness results
• Efficient Algorithms for Regular Expression Constrained Sequence Alignment
• Regular expression constrained sequence alignment
• Regular language constrained sequence alignment revisited
• Translating regular expressions into small \(\epsilon\)-free nondeterministic finite automata

Cited in

(9)

• Algorithms for path-constrained sequence alignment
• Combinatorial Pattern Matching
• Regular expression constrained sequence alignment
• SA-REPC -- sequence alignment with regular expression path constraint
• Regular language constrained sequence alignment revisited
• Approximate regular expression pattern matching with concave gap penalties
• Efficient Algorithms for Regular Expression Constrained Sequence Alignment
• Efficient algorithms for regular expression constrained sequence alignment
• Counting regular expressions in degenerated sequences through lazy Markov chain embedding

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Uses Software

• PROSITE

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