Bioinformatics algorithms. Sequence analysis, genome rearrangements, and phylogenetic reconstruction

zbMATH Open1295.92011MaRDI QIDQ5397902FDOQ5397902

Authors: Enno Ohlebusch 

Publication date: 25 February 2014

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zbMATH Keywords

quartetssequence analysisphylogenetic reconstructionrange minimum queriesstring comparisonwavelet treesmultiple sequence alignmentsplitsbidirectional searchapproximate string matchingKnuth-Morris-Pratt algorithmexact string matchingBurrows-Wheeler transformmaximal repeatsgenome rearrangementslowest common ancestorstring kernelsultrametric distanceLempel-Ziv factorizationAho-Corasick algorithmrepeatswhole genome alignmentpairwise sequence alignmentBoyer-Moore-Horspool algorithmLCP-arraybioinformatics algorithmscompressed full text indexescompressed suffix and LCP arraysenhanced suffix arraysLCP-interval treemultiple string comparisonneighbour joining algorithmsnon-additive dissimilarity matricesreversals sortingspace efficient string comparisontransversals with suffix linksUPGMA algorithm

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Problems related to evolution (92D15) Protein sequences, DNA sequences (92D20) Research exposition (monographs, survey articles) pertaining to biology (92-02) Computational methods for problems pertaining to biology (92-08) General biology and biomathematics (92B05) Algorithms on strings (68W32)

Cited In (42)

• Full-text indexes for high-throughput sequencing
• Genome-Scale Algorithm Design
• Bioinformatics Algorithms
• Edge minimization in de Bruijn graphs
• String inference from longest-common-prefix array
• LCP array construction in external memory
• A simple algorithm for computing the document array
• Engineering a lightweight external memory suffix array construction algorithm
• Algorithms for genomics analysis
• Algorithmic aspects of bioinformatics. Translated from the German original
• On the optimisation of the GSACA suffix array construction algorithm
• Online LZ77 parsing and matching statistics with RLBWTs
• Lyndon array construction during Burrows-Wheeler inversion
• Algorithms to compute the Burrows-Wheeler similarity distribution
• Lightweight LCP construction for very large collections of strings
• Computing the original eBWT faster, simpler, and with less memory
• An improved algorithm for the all-pairs suffix-prefix problem
• Genome sequencing technology and algorithms.
• Better external memory LCP array construction
• Efficient construction of the BWT for repetitive text using string compression
• Algorithms in bioinformatics. A practical introduction.
• Optimal suffix sorting and LCP array construction for constant alphabets
• Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret
• Efficient construction of a compressed de Bruijn graph for pan-genome analysis
• Space-efficient parallel construction of succinct representations of suffix tree topologies
• ReCombinatorics. The algorithmics of ancestral recombination graphs and explicit phylogenetic networks. With contributions from Charles H. Langley, Yun S. Song and Yufeng Wu
• Alphabet-independent algorithms for finding context-sensitive repeats in linear time
• Comparative genomics with succinct colored de Bruijn graphs
• Tighter bounds for the sum of irreducible LCP values
• Parallel computation of the Burrows Wheeler transform in compact space
• Reporting consecutive substring occurrences under bounded gap constraints
• Faster compressed suffix trees for repetitive collections
• Tighter bounds for the sum of irreducible LCP values
• Burrows-Wheeler transform and LCP array construction in constant space
• Inducing the Lyndon array
• Solving string problems on graphs using the labeled direct product
• The longest common substring problem
• On the string matching with \(k\) mismatches
• Title not available (Why is that?)
• Linking indexing data structures to de Bruijn graphs: construction and update
• Inducing enhanced suffix arrays for string collections
• A practical semi-external memory method for approximate pattern matching

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