Efficient pattern matching for RNA secondary structures

DOI10.1016/j.tcs.2015.05.016zbMath1331.92117OpenAlexW261595532MaRDI QIDQ500967

Richard Beal, Donald A. Adjeroh

Publication date: 8 October 2015

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

Full work available at URL: https://doi.org/10.1016/j.tcs.2015.05.016

zbMATH Keywords

RNAstructural matchingstructural string\(s\)-match\(s\)-string\(s\)-suffix arrayRNA structure motifsstructural suffix array

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Data structures (68P05) Algorithms on strings (68W32)

Related Items (4)

Practical space-efficient index for structural pattern matching ⋮ Compressed parameterized pattern matching ⋮ A prefix array for parameterized strings ⋮ A brief history of parameterized matching problems

Uses Software

• CONTRAfold

Cites Work

• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Parameterized longest previous factor
• The longest common subsequence problem for arc-annotated sequences
• Combinatorics of RNA secondary structures
• Spaces of RNA secondary structures
• Alphabet dependence in parameterized matching
• Suffix-sorting via Shannon-Fano-Elias codes
• Algorithms for pattern matching and discovery in RNA secondary structure
• Exact matching of RNA secondary structure patterns
• Generalization of a suffix tree for RNA structural pattern matching
• \(p\)-suffix sorting as arithmetic coding
• On-line construction of parameterized suffix trees for large alphabets
• Fast detection of common sequence structure patterns in RNAs
• The affix array data structure and its applications to RNA secondary structure analysis
• Pattern matching for arc-annotated sequences
• Suffix Arrays: A New Method for On-Line String Searches
• Faster suffix tree construction with missing suffix links
• Lightweight Parameterized Suffix Array Construction
• New approaches for computer analysis of nucleic acid sequences.
• A Note on the Height of Suffix Trees
• Algorithms on Strings, Trees and Sequences
• A theory of parameterized pattern matching

This page was built for publication: Efficient pattern matching for RNA secondary structures