Parametric optimization of sequence alignment
DOI10.1007/BF01185430zbMATH Open0802.92016OpenAlexW2018885841MaRDI QIDQ1336962FDOQ1336962
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
Recommendations
DNA sequencesdynamic programminggapsmismatchesspacesconvex decompositionlocal alignmentvariable weightsamino acid sequencesmatchesglobal alignmentoptimal sequence alignmentcomputer program PARALparametric sequence alignmentsequence homologyweighted minimum edit distance
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)
Cites Work
- Combinatorial Optimization with Rational Objective Functions
- Parametric Combinatorial Computing and a Problem of Program Module Distribution
- Mathematical Techniques for Efficient Record Segmentation in Large Shared Databases
- An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules
- Title not available (Why is that?)
- Optimal sequence alignment allowing for long gaps
Cited In (28)
- 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
- Inverse parametric sequence alignment
- Parametric multiple sequence alignment and phylogeny construction
- Title not available (Why is that?)
- Lower bounds for optimal alignments of binary sequences
- Bounds for parametric sequence comparison
- Title not available (Why is that?)
- 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
- Title not available (Why is that?)
- Optimality regions and fluctuations for Bernoulli last passage models
- Parametric and ensemble sequence alignment algorithms
- Parametric sequence alignment with constraints
- Consistency of optimal sequence alignments
- Optimal sequence alignment allowing for long gaps
- 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
- Title not available (Why is that?)
- Simple and Fast Inverse Alignment
- Extended pairwise local alignment of wild card DNA/RNA sequences using dynamic programming
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