Approximate All-Pairs Suffix/Prefix Overlaps

DOI10.1007/978-3-642-13509-5_8MaRDI QIDQ3575238zbMATH OpenOpenAlexFDO

Authors Niko Välimäki, Veli Mäkinen, Susana Ladra

Publication date 26 July 2010

Published in Combinatorial Pattern Matching (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-642-13509-5_8

Mathematics Subject Classification ID

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

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Cited in

(9)

• Computing the multi-string BWT and LCP array in external memory
• Computing the Burrows-Wheeler transform of a string and its reverse in parallel
• Least random suffix/prefix matches in output-sensitive time
• Fast and simple computations using prefix tables under Hamming and edit distance
• Approximate all-pairs suffix/prefix overlaps
• Linear-time computation of prefix table for weighted strings {\&} applications
• Simulating the DNA overlap graph in succinct space
• Computing all-vs-all MEMs in run-length-encoded collections of HiFi reads
• Computational graph pangenomics: a tutorial on data structures and their applications

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