A polyhedral approach to sequence alignment problems
DOI10.1016/S0166-218X(00)00194-3zbMATH Open0998.92017OpenAlexW2125372717WikidataQ56977389 ScholiaQ56977389MaRDI QIDQ1585327FDOQ1585327
Authors: John D. Kececioglu, Hans-Peter Lenhof, K. Mehlhorn, Petra Mutzel, Knut Reinert, Martin Vingron 
Publication date: 13 November 2002
Published in: Discrete Applied Mathematics (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1016/s0166-218x(00)00194-3
Recommendations
- Research in Computational Molecular Biology
- Approximation algorithms for multiple sequence alignment
- On the complexity of constrained sequences alignment problems
- An optimization approach to multiple sequence alignment
- Algorithms for path-constrained sequence alignment
- The parameterized complexity of sequence alignment and consensus
- Dynamic programming based approximation algorithms for sequence alignment with constraints
- A fast algorithm for the constrained multiple sequence alignment problem
- An algorithm and applications to sequence alignment with weighted constraints
Applications of graph theory (05C90) Complexity and performance of numerical algorithms (65Y20) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Combinatorial optimization (90C27)
Cites Work
- Title not available (Why is that?)
- Properties of vertex packing and independence system polyhedra
- Optimization of a 532-city symmetric traveling salesman problem by branch and cut
- The ellipsoid method and its consequences in combinatorial optimization
- Title not available (Why is that?)
- Facet of regular 0–1 polytopes
- A New Algorithm for Generating All the Maximal Independent Sets
- Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems
- Title not available (Why is that?)
- A Cutting Plane Algorithm for the Linear Ordering Problem
- Title not available (Why is that?)
- Title not available (Why is that?)
- The Context Dependent Comparison of Biological Sequences
- Generalized sequence alignment and duality
- Title not available (Why is that?)
- On Linear Characterizations of Combinatorial Optimization Problems
- Locally optimal subalignments using nonlinear similarity functions
- Multiple sequence comparison and consistency on multipartite graphs
- Title not available (Why is that?)
- Multiple DNA and protein sequence alignment based on segment-to-segment comparison.
Cited In (21)
- On the complexity of sequence to graph alignment
- Partially local multi-way alignments
- On some optimization problems in molecular biology
- A Subquadratic Sequence Alignment Algorithm for Unrestricted Scoring Matrices
- Exact Multiple Sequence Alignment by Synchronized Decision Diagrams
- DC programming and DCA for challenging problems in bioinformatics and computational biology
- Novel evolutionary models and applications to sequence alignment problems
- DCA based algorithms for multiple sequence alignment (MSA)
- A path selection approach to global pairwise sequence alignment using integer linear optimization†
- A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences
- Global pairwise sequence alignment through mixed-integer linear programming: a template-free approach
- A Lagrangian relaxation approach for the multiple sequence alignment problem
- Heuristic algorithms in computational molecular biology
- An exact mathematical programming approach to multiple RNA sequence-structure alignment
- Near optimal multiple alignment within a band in polynomial time
- New formulations of the multiple sequence alignment problem
- The maximum weight trace alignment merging problem
- Fast separation for the three-index assignment problem
- Molecular alignment as a penalized permutation Procrustes problem
- Sequence alignment with arbitrary steps and further generalizations, with applications to alignments in linguistics
- Mathematical programming in computational biology: an annotated bibliography
Uses Software
This page was built for publication: A polyhedral approach to sequence alignment problems
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q1585327)
