IDPM: An Improved Degenerate Pattern Matching Algorithm for Biological Sequences

DOI10.1142/S0129054117500307zbMath1387.68314OpenAlexW2788691712WikidataQ63565682 ScholiaQ63565682MaRDI QIDQ4639924

E. James Harner, Binghua Jiang, Don A. Adjeroh, Yue Jiang, Jie Lin

Publication date: 14 May 2018

Published in: International Journal of Foundations of Computer Science (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1142/s0129054117500307

zbMATH Keywords

bioinformaticspattern matchingDNA sequenceprotein sequenceBoyer-Moore algorithmdegenerate pattern

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Algorithms on strings (68W32)

Uses Software

• ClustalW

Cites Work

• A new approach to pattern matching in degenerate DNA/RNA sequences and distributed pattern matching
• Fast pattern-matching on indeterminate strings
• Covering problems for partial words and for indeterminate strings
• Inferring an indeterminate string from a prefix graph
• A fast string searching algorithm
• Identity-Based Encryption Gone Wild
• AN ADAPTIVE HYBRID PATTERN-MATCHING ALGORITHM ON INDETERMINATE STRINGS
• Generalized String Matching
• Approximate Boyer–Moore String Matching
• Efficient string matching
• Algorithms on Strings, Trees and Sequences
• Tree Pattern Matching to Subset Matching in Linear Time
• Algorithmic Combinatorics on Partial Words
• Average case analysis of the Boyer‐Moore algorithm
• Combinatorial Pattern Matching
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