Unified View of Backward Backtracking in Short Read Mapping

DOI10.1007/978-3-642-12476-1_13MaRDI QIDQ3558271zbMATH OpenOpenAlexFDO

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

zbMATH Keywords

compressed data structuresfull-text indexingpersonal genomics

Mathematics Subject Classification ID

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

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Cited in

(9)

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

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