A new approach to pattern matching in degenerate DNA/RNA sequences and distributed pattern matching

DOI10.1007/S11786-007-0029-ZMaRDI QIDQ942989zbMATH OpenOpenAlexFDO

Authors Costas S. Iliopoulos, L. Mouchard, M. Sohel Rahman

Publication date 8 September 2008

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

Full work available at URL https://doi.org/10.1007/s11786-007-0029-z

zbMATH Keywords

algorithmpattern matchingdegenerate stringsDNA/RNA sequences

Mathematics Subject Classification ID

Pattern recognition, speech recognition (68T10) Analysis of algorithms and problem complexity (68Q25) Nonnumerical algorithms (68W05)

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Cited in

(17)

• Filtering degenerate patterns with application to protein sequence analysis
• Monge properties of sequence alignment
• An aperiodicity problem for multiwords
• Computing regularities in strings: a survey
• EFFICIENT ALGORITHMS FOR DEGENERATE PRIMER SEARCH
• Some string matching problems from bioinformatics which still need better solutions
• Indeterminate string factorizations and degenerate text transformations
• On-line string matching in highly similar DNA sequences
• Elastic-Degenerate String Matching via Fast Matrix Multiplication
• Indeterminate string inference algorithms
• Indexing a sequence for mapping reads with a single mismatch
• An efficient algorithm to detect palindromes in DNA sequences using periodicity transform
• Efficient pattern matching in degenerate strings with the Burrows-Wheeler transform
• A new approach to regular \& indeterminate strings
• IDPM: an improved degenerate pattern matching algorithm for biological sequences
• Inferring an indeterminate string from a prefix graph
• Subset Seed Automaton

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