Parametric optimization of sequence alignment

DOI10.1007/BF01185430MaRDI QIDQ1336962zbMATH OpenOpenAlexFDO

Authors Dan Gusfield, K. Balasubramanian, Dalit Naor

Publication date 8 November 1994

Published in Algorithmica (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/bf01185430

zbMATH Keywords

amino acid sequencescomputer program PARALconvex decompositionDNA sequencesdynamic programminggapsglobal alignmentlocal alignmentmatchesmismatchesoptimal sequence alignmentparametric sequence alignmentsequence homologyspacesvariable weightsweighted minimum edit distance

Mathematics Subject Classification ID

Abstract computational complexity for mathematical programming problems (90C60) Applications of mathematical programming (90C90) Computational methods for problems pertaining to biology (92-08) Protein sequences, DNA sequences (92D20)

Recommendations

• scientific article; zbMATH DE number 434724
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Cites work

• An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules
• Combinatorial Optimization with Rational Objective Functions
• scientific article; zbMATH DE number 742991 (Why is no real title available?)
• Mathematical Techniques for Efficient Record Segmentation in Large Shared Databases
• Optimal sequence alignment allowing for long gaps
• Parametric Combinatorial Computing and a Problem of Program Module Distribution

Cited in

(30)

• Efficient optimal decomposition of a sequence into disjoint regions, each matched to some template in an inventory
• Parametric and ensemble sequence alignment algorithms
• Classes of cost functions for string edit distance
• Bounds for parametric sequence comparison
• Optimality regions and fluctuations for Bernoulli last passage models
• scientific article; zbMATH DE number 1615271 (Why is no real title available?)
• scientific article; zbMATH DE number 434724 (Why is no real title available?)
• Simple and Fast Inverse Alignment
• Monge properties of sequence alignment
• On the structure of RNA branching polytopes
• scientific article; zbMATH DE number 742991 (Why is no real title available?)
• scientific article; zbMATH DE number 2089964 (Why is no real title available?)
• Inverse parametric sequence alignment
• Bounded-length Smith-Waterman alignment
• Extended pairwise local alignment of wild card DNA/RNA sequences using dynamic programming
• Parametric analysis of RNA branching configurations
• Parametric analysis of alignment and phylogenetic uncertainty
• Tropical geometry of statistical models
• Parametric inference for biological sequence analysis
• The Relative Inefficiency of Sequence Weights Approaches in Determining a Nucleotide Position Weight Matrix
• Parametric sequence alignment with constraints
• Alignment networks and electrical networks
• A stronger lower bound on parametric minimum spanning trees
• Parametric maximum parsimonious reconstruction on trees
• How much data is sufficient to learn high-performing algorithms?
• Line geometries for sequence comparisons
• Parametric multiple sequence alignment and phylogeny construction
• Optimal sequence alignment allowing for long gaps
• Consistency of optimal sequence alignments
• Lower bounds for optimal alignments of binary sequences

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