IDPM: an improved degenerate pattern matching algorithm for biological sequences

DOI10.1142/S0129054117500307MaRDI QIDQ4639924zbMATH OpenOpenAlexWikidataFDO

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

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

bioinformaticsBoyer-Moore algorithmdegenerate patternDNA sequencepattern matchingprotein sequence

Mathematics Subject Classification ID

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

Recommendations

• A new approach to pattern matching in degenerate DNA/RNA sequences and distributed pattern matching
• Efficient pattern matching in degenerate strings with the Burrows-Wheeler transform
• Faster Online Elastic Degenerate String Matching

Cites work

• A fast string searching algorithm
• A new approach to pattern matching in degenerate DNA/RNA sequences and distributed pattern matching
• Algorithmic Combinatorics on Partial Words
• Algorithms on Strings, Trees and Sequences
• An adaptive hybrid pattern-matching algorithm on indeterminate strings
• Approximate Boyer–Moore String Matching
• Average case analysis of the Boyer‐Moore algorithm
• Combinatorial Pattern Matching
• Efficient string matching
• Fast pattern-matching on indeterminate strings
• Generalized String Matching
• scientific article; zbMATH DE number 3471577 (Why is no real title available?)
• scientific article; zbMATH DE number 3619307 (Why is no real title available?)
• scientific article; zbMATH DE number 1305413 (Why is no real title available?)
• scientific article; zbMATH DE number 2052918 (Why is no real title available?)
• Identity-Based Encryption Gone Wild
• Inferring an indeterminate string from a prefix graph
• Tree Pattern Matching to Subset Matching in Linear Time

Cited in

(4)

• Filtering degenerate patterns with application to protein sequence analysis
• Efficient pattern matching in degenerate strings with the Burrows-Wheeler transform
• EFFICIENT ALGORITHMS FOR DEGENERATE PRIMER SEARCH
• A new approach to pattern matching in degenerate DNA/RNA sequences and distributed pattern matching

Describes a project that uses

Uses Software

• ClustalW

This page was built for publication: IDPM: an improved degenerate pattern matching algorithm for biological sequences

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q4639924)