Approximate search of short patterns with high error rates using the \(01^\ast 0\) lossless seeds

DOI10.1016/j.jda.2016.03.002zbMath1362.68306OpenAlexW2301420365MaRDI QIDQ2628801

Hélène Touzet, Mikaël Salson, Christophe Vroland, Sébastien Bini

Publication date: 15 July 2016

Published in: Journal of Discrete Algorithms (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jda.2016.03.002

zbMATH Keywords

approximate string matchingcomputational biologyLevenshtein distancelossless approximate seeds

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Algorithms on strings (68W32)

Uses Software

• miRBase
• SeqAn
• PatternHunter
• RazerS
• Bowtie 2
• BWA

Cites Work

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• A linear size index for approximate pattern matching
• Text indexing with errors
• Approximate string matching with compressed indexes
• On spaced seeds for similarity search
• Fast and practical approximate string matching
• Versatile Succinct Representations of the Bidirectional Burrows-Wheeler Transform
• Compressed representations of sequences and full-text indexes
• Lossless Seeds for Searching Short Patterns with High Error Rates
• Subset Seed Automaton
• Indexing compressed text
• Unified View of Backward Backtracking in Short Read Mapping
• Bidirectional Search in a String with Wavelet Trees
• The String-to-String Correction Problem
• Approximate String Matching Using a Bidirectional Index
• Faster Filters for Approximate String Matching
• Compressed text indexes

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