Unified View of Backward Backtracking in Short Read Mapping

DOI10.1007/978-3-642-12476-1_13zbMATH Open1284.92075OpenAlexW1802152036MaRDI QIDQ3558271FDOQ3558271

Authors: Veli Mäkinen, Niko Välimäki, Antti Laaksonen, Riku Katainen 

Publication date: 4 May 2010

Published in: Algorithms and Applications (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/978-3-642-12476-1_13

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zbMATH Keywords

full-text indexingcompressed data structurespersonal genomics

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Data structures (68P05)

Cited In (9)

• Multi-pattern matching with bidirectional indexes
• Methods for allocating ambiguous short-reads
• Approximate all-pairs suffix/prefix overlaps
• Approximate search of short patterns with high error rates using the \(01^\ast 0\) lossless seeds
• SpliceTAPyR -- an efficient method for transcriptome alignment
• Designing efficient spaced seeds for SOLiD read mapping
• Analysis of min-hashing for variant tolerant DNA read mapping
• Exact sketch-based read mapping
• G-MAPSEQ -- a new method for mapping reads to a reference genome

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