Extending alignments with \(k\)-mismatches and \(\ell\)-gaps

DOI10.1016/j.tcs.2013.06.012zbMath1290.68143OpenAlexW2081934847MaRDI QIDQ2437749

Laurent Mouchard, Costas S. Iliopoulos, Carl Barton, Solon P. Pissis, Inbok Lee, Kun Soo Park

Publication date: 13 March 2014

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

Full work available at URL: https://doi.org/10.1016/j.tcs.2013.06.012

zbMATH Keywords

dynamic programmingalgorithms on stringspairwise sequence alignment

Mathematics Subject Classification ID

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

Uses Software

• Soap
• libgapmis
• BWA

Cites Work

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• Approximate string matching with suffix automata
• Data structures and algorithms for approximate string matching
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• Generalized String Matching
• The theory and computation of evolutionary distances: Pattern recognition
• On the Theory and Computation of Evolutionary Distances
• An Extension of the String-to-String Correction Problem
• A technique for isolating differences between files
• The String-to-String Correction Problem
• Algorithms For Computing Approximate Repetitions In Musical Sequences
• Matching Sequences under Deletion/Insertion Constraints

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