General methods of sequence comparison
From MaRDI portal
Publication:799527
DOI10.1007/BF02459498zbMath0548.92006OpenAlexW4241051276MaRDI QIDQ799527
Publication date: 1984
Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1007/bf02459498
Applications of mathematical programming (90C90) Dynamic programming (90C39) Software, source code, etc. for problems pertaining to biology (92-04) Physiological, cellular and medical topics (92Cxx)
Related Items
Optimized homology searches of the gene and protein sequence data banks ⋮ Parametric and ensemble sequence alignment algorithms ⋮ A differential geometric treatment of protein structure comparison ⋮ Locally optimal subalignments using nonlinear similarity functions ⋮ Approximate regular expression pattern matching with concave gap penalties ⋮ Graph nodes and a definition of structural similarity ⋮ Set-spectrum method in structure comparison and the concept of topological kinship ⋮ Computing orbits of the automorphism group of the subsequence poset \(B_{ m, n }\) ⋮ The alignment of protein structures in three dimensions ⋮ Algorithms for the optimal identification of segment neighborhoods ⋮ Posets of shuffles ⋮ Sequence Alignments with Matched Sections ⋮ Approximate matching of regular expressions ⋮ On posets of \(m\)-ary words ⋮ Speeding up dynamic programming with applications to molecular biology ⋮ On locally optimal alignments in genetic sequences ⋮ Multiple sequence comparison -- a peptide matching approach ⋮ On an alternative sequence comparison statistic of Steele ⋮ Minimum message length encoding and the comparison of macromolecules ⋮ On the number of alignments of k sequences ⋮ Distribution of the number of matches between nucleotide sequences ⋮ Letter change bias and local uniqueness in optimal sequence alignments ⋮ New method for global alignment of 2 DNA sequences by the tree data structure ⋮ Thermodynamical approach to the longest common subsequence problem ⋮ Large deviations-based upper bounds on the expected relative length of longest common subsequences ⋮ Approximately matching context-free languages ⋮ A local algorithm for DNA sequence alignment with inversions ⋮ A survey of multiple sequence comparison methods ⋮ Poisson, compound Poisson and process approximations for testing statistical significance in sequence comparisons ⋮ Sparse long blocks and the micro-structure of the longuest common subsequences ⋮ A bit-string longest-common-subsequence algorithm ⋮ Comparison of strings belonging to the same family ⋮ Pattern recognition in several sequences: Consensus and alignment ⋮ A dynamic programming algorithm to find all solutions in a neighborhood of the optimum ⋮ Stanislaw M. Ulam's contributions to theoretical biology
Cites Work
- Unnamed Item
- Unnamed Item
- Unnamed Item
- An extreme value theory for sequence matching
- Comparison of biosequences
- Matching code sequences utilizing context free quality measures
- Some biological sequence metrics
- A molecular sequence metric and evolutionary trees
- An algorithm for the distance between two finite sequences
- Shortcuts, diversions, and maximal chains in partially ordered sets
- Multidimensional Scaling, Tree-Fitting, and Clustering
- Technical Note—Determining All Optimal and Near-Optimal Solutions when Solving Shortest Path Problems by Dynamic Programming
- The Context Dependent Comparison of Biological Sequences
- An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules
- Sequence alignments in the neighborhood of the optimum with general application to dynamic programming
- New approaches for computer analysis of nucleic acid sequences.
- Algorithms for approximate string matching
- The theory and computation of evolutionary distances: Pattern recognition
- Asymptotic Limits for a Two-Dimensional Recursion
- On the Theory and Computation of Evolutionary Distances
- Minimal Mutation Trees of Sequences
- Sequence comparison by dynamic programming
- Pattern recognition in genetic sequences
- Note on a “Square” Functional Equation
- Matching Sequences under Deletion/Insertion Constraints
- A sequence-comparison statistic and algorithm