Regular expression constrained sequence alignment

DOI10.1016/J.JDA.2007.01.003MaRDI QIDQ925058zbMATH OpenOpenAlexFDO

Authors Abdullah N. Arslan

Publication date 29 May 2008

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

Full work available at URL https://doi.org/10.1016/j.jda.2007.01.003

zbMATH Keywords

dynamic programmingpattern matchingsequence alignmentfinite automatonregular expression

Mathematics Subject Classification ID

Formal languages and automata (68Q45) Protein sequences, DNA sequences (92D20) Dynamic programming (90C39) Combinatorics on words (68R15) Algorithms on strings (68W32)

Recommendations

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

Cites work

• scientific article; zbMATH DE number 3664335 (Why is no real title available?)
• scientific article; zbMATH DE number 699389 (Why is no real title available?)
• A simple algorithm for the constrained sequence problems
• ALGORITHMS FOR THE CONSTRAINED LONGEST COMMON SUBSEQUENCE PROBLEMS
• Algorithms for the Longest Common Subsequence Problem
• Approximate matching of regular expressions
• The constrained longest common subsequence problem

Cited in

(11)

• Efficient Algorithms for Regular Expression Constrained Sequence Alignment
• Combinatorial Pattern Matching
• Efficient algorithms for regular expression constrained sequence alignment
• Computing longest common square subsequences
• A hardness result and new algorithm for the longest common palindromic subsequence problem
• Fast algorithms for computing the constrained LCS of run-length encoded strings
• SA-REPC -- sequence alignment with regular expression path constraint
• Algorithms for path-constrained sequence alignment
• Regular language constrained sequence alignment revisited
• Approximate regular expression pattern matching with concave gap penalties
• Practical regular expression constrained sequence alignment

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Uses Software

• MuSiC

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