Algorithms on Strings, Trees and Sequences
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alignmentsbioinformaticscomputational biologyDNA sequencingdynamic programmingedit distanceevolutionary treessequence databasesstring matchingsuffix trees
Introductory exposition (textbooks, tutorial papers, etc.) pertaining to computer science (68-01) Analysis of algorithms and problem complexity (68Q25) Combinatorics on words (68R15) Computing methodologies for text processing; mathematical typography (68U15) Nonnumerical algorithms (68W05) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)
Recommendations
- Algorithms on Strings
- String algorithms. Papers based on the presentations at four meetings, London algorithms workshop, December 2000; London stringology day, February 2003; Rouen sequence algorithmics, June 2002; Patras stringology days, February 2004.
- scientific article; zbMATH DE number 828444
- Algorithmic aspects of bioinformatics. Translated from the German original
Cited in
(only showing first 100 items - show all)- Semi-local longest common subsequences in subquadratic time
- Quasi-median hulls in Hamming space are Steiner hulls
- On the tiling by translation problem
- Faster pattern matching with character classes using prime number encoding
- \(k\)-difference matching in amortized linear time for all the words in a text
- Linearized suffix tree: An efficient index data structure with the capabilities of suffix trees and suffix arrays
- Investigation of accelerated search for close text sequences with the help of vector representations
- A Lagrangian relaxation approach for the multiple sequence alignment problem
- Phylogenetic graph models beyond trees
- Discovering subword associations in strings in time linear in the output size
- Approximation algorithms for constrained generalized tree alignment problem
- Determining the consistency of partial tree descriptions
- Sparse LCS common substring alignment
- Computing the longest topological common subsequence of a symbol-wise totally ordered directed acyclic graph and a sequence
- Alignments with non-overlapping moves, inversions and tandem duplications in \(O(n^{4})\) time
- Repetitions in strings: algorithms and combinatorics
- Recognition of the structural-functional organization of genetic sequences
- Temporal similarity by measuring possibilistic uncertainty in CBR
- Faster entropy-bounded compressed suffix trees
- Searching for gapped palindromes
- Data compression for proof replay
- Average-optimal string matching
- A new method for approximate indexing and dictionary lookup with one error
- The greedy algorithm for edit distance with moves
- PRISM: an effective approach for frequent sequence mining via prime-block encoding
- Graph traversals, genes and matroids: An efficient case of the travelling salesman problem
- Parallel construction and query of index data structures for pattern matching on square matrices
- Approximate symbolic pattern matching for protein sequence data
- Non-approximability of weighted multiple sequence alignment.
- Generalizations of suffix arrays to multi-dimensional matrices.
- Finding approximate repetitions under Hamming distance.
- Truncated suffix trees and their application to data compression.
- Recent progress on selected topics in database research. -- A report by nine young Chinese researchers working in the United States.
- Combinatorics of periods in strings.
- Algorithmic complexity of protein identification: Combinatorics of weighted strings
- RNA secondary structure comparison: Exact analysis of the Zhang-Shasha tree edit algorithm.
- Hardness of approximation for non-overlapping local alignments.
- Distinguishing string selection problems.
- The shortest path problem with forbidden paths
- Approximation algorithms for the shortest total path length spanning tree problem
- Repetitive perhaps, but certainly not boring
- Fixed topology alignment with recombination
- Efficient data reconciliation
- Bounds for parametric sequence comparison
- On maximal repeats in strings
- Quasi-median graphs from sets of partitions
- Extended suffix array construction using Lyndon factors
- Improved upper bounds on all maximal -gapped repeats and palindromes
- A substring-substring LCS data structure
- Space-efficient indexes for forbidden extension queries
- Computing longest common extensions in partial words
- An improved approximation algorithm for the discrete Fréchet distance
- Fast structural alignment of biomolecules using a hash table, n-grams and string descriptors
- Approximate string matching with compressed indexes
- Suffix-sorting via Shannon-Fano-Elias codes
- A fast algorithm for the all-pairs suffix-prefix problem
- Exact solution to median surface problem using 3D graph search and application to parameter space exploration
- Border correlations, lattices, and the subgraph component polynomial
- Longest common extension
- Searching of gapped repeats and subrepetitions in a word
- On finding a longest common palindromic subsequence
- Tighter bounds and optimal algorithms for all maximal -gapped repeats and palindromes. Finding all maximal -gapped repeats and palindromes in optimal worst case time on integer alphabets
- On the number of gapped repeats with arbitrary gap
- Efficient algorithms for computing the inner edit distance of a regular language via transducers
- Hide and seek with repetitions
- A novel statistical measure for sequence comparison on the basis of \(k\)-word counts
- An efficient algorithm for LCS problem between two arbitrary sequences
- Edit distance with block deletions
- The smallest grammar problem as constituents choice and minimal grammar parsing
- Practical compressed suffix trees
- Sublinear time motif discovery from multiple sequences
- Modeling dynamic programming problems over sequences and trees with inverse coupled rewrite systems
- A faster quick search algorithm
- A new decomposition technique for maximal clique enumeration for sparse graphs
- \(xkcd\)-repeats: a new taxonomy of repeats defined by their context diversity
- Computing regularities in strings: a survey
- Computing the longest previous factor
- Exploiting word-level parallelism for fast convolutions and their applications in approximate string matching
- On-line construction of compact directed acyclic word graphs
- Linear time algorithms for finding and representing all the tandem repeats in a string
- Combinatorics and algorithms for low-discrepancy roundings of a real sequence
- Partial words and the critical factorization theorem
- Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination
- An inexact-suffix-tree-based algorithm for detecting extensible patterns
- Algorithms for pattern matching and discovery in RNA secondary structure
- Exact matching of RNA secondary structure patterns
- Ranked document retrieval for multiple patterns
- The suffix binary search tree and suffix AVL tree
- Reducing space for index implementation.
- Finding approximate palindromes in strings
- Weighted sequence graphs: Boosting iterated dynamic programming using locally suboptimal solutions
- Finding similar regions in many sequences
- Discovering instances of poetic allusion from anthologies of classical Japanese poems
- Tabular parsing and algebraic transformations
- The longest common subsequence problem for sequences with nested arc annotations.
- Approximate pattern matching and transitive closure logics.
- The haplotyping problem: an overview of computational models and solutions
- A space-efficient algorithm for sequence alignment with inversions and reversals
- Two-dimensional pattern matching with rotations
- Computing the similarity of two sequences with nested arc annotations
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