Parametric optimization of sequence alignment

DOI10.1007/BF01185430zbMath0802.92016OpenAlexW2018885841MaRDI QIDQ1336962

K. Balasubramanian, Dan Gusfield, 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

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

Related Items (13)

Classes of cost functions for string edit distance ⋮ On the Structure of RNA Branching Polytopes ⋮ Optimality regions and fluctuations for Bernoulli last passage models ⋮ Parametric multiple sequence alignment and phylogeny construction ⋮ Parametric maximum parsimonious reconstruction on trees ⋮ A stronger lower bound on parametric minimum spanning trees ⋮ Lower bounds for optimal alignments of binary sequences ⋮ Parametric analysis of RNA branching configurations ⋮ Parametric analysis of alignment and phylogenetic uncertainty ⋮ Unnamed Item ⋮ Tropical geometry of statistical models ⋮ Parametric inference for biological sequence analysis ⋮ Bounds for parametric sequence comparison

Cites Work

• Optimal sequence alignment allowing for long gaps
• An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules
• Parametric Combinatorial Computing and a Problem of Program Module Distribution
• Combinatorial Optimization with Rational Objective Functions
• Mathematical Techniques for Efficient Record Segmentation in Large Shared Databases
• Unnamed Item

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