DCA based algorithms for multiple sequence alignment (MSA)

DOI10.1007/S10100-013-0324-5MaRDI QIDQ301241zbMATHOpenAlexFDO

Authors Le Thi Hoai An, Pham Dinh Tao, Moulay Taïb Belghiti

Publication date 30 June 2016

Published in CEJOR. Central European Journal of Operations Research (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/s10100-013-0324-5

zbMATH Keywords

DCAbinary linear programmingconstraint generationDC programmingexact penaltymaximum weight tracemultiple sequence alignment

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Protein sequences, DNA sequences (92D20) Integer programming (90C10) Algorithms on strings (68W32)

Recommendations

• DC programming and DCA for challenging problems in bioinformatics and computational biology
• New formulations of the multiple sequence alignment problem
• An optimization approach to multiple sequence alignment
• An approximation algorithm for alignment of multiple sequences using motif discovery
• A New Dynamic Programming Algorithm for Multiple Sequence Alignment

Cites work

• scientific article; zbMATH DE number 53467 (Why is no real title available?)
• scientific article; zbMATH DE number 3567782 (Why is no real title available?)
• A D.C. Optimization Algorithm for Solving the Trust-Region Subproblem
• A new efficient algorithm based on DC programming and DCA for clustering
• A polyhedral approach to sequence alignment problems
• Algorithms on Strings, Trees and Sequences
• Convex Analysis
• Convex analysis approach to d. c. programming: Theory, algorithms and applications
• Efficient algorithms for local alignment search
• Efficient algorithms for similarity search
• Exact penalty in d. c. programming
• Integer quadratic programming models in computational biology
• Large-Scale Molecular Optimization from Distance Matrices by a D.C. Optimization Approach
• Nonlinear wavelet image processing: variational problems, compression, and noise removal through wavelet shrinkage
• Solving a class of linearly constrained indefinite quadratic problems by DC algorithms
• The Concave-Convex Procedure
• The DC (Difference of convex functions) programming and DCA revisited with DC models of real world nonconvex optimization problems

Cited in

(5)

• DC programming and DCA: thirty years of developments
• DC programming and DCA for challenging problems in bioinformatics and computational biology
• Recent advances in computational biology, bioinformatics, medicine, and healthcare by modern OR
• Comparison of two algorithms of direct coupling analysis of protein
• DC programming and DCA for general DC programs

Describes a project that uses

Uses Software

• Balibase
• ClustalW
• T-coffee

This page was built for publication: DCA based algorithms for multiple sequence alignment (MSA)

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q301241)