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

DNA sequencesdynamic programminggapsmismatchesspacesconvex decompositionlocal alignmentvariable weightsamino acid sequencesmatchesglobal alignmentoptimal sequence alignmentcomputer program PARALparametric sequence alignmentsequence homologyweighted minimum edit distance

Mathematics Subject Classification ID

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

Recommendations

• scientific article; zbMATH DE number 434724
• Bounds for parametric sequence comparison
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Cites work

• scientific article; zbMATH DE number 742991 (Why is no real title available?)
• An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules
• Combinatorial Optimization with Rational Objective Functions
• 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

(28)

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

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