Global pairwise sequence alignment through mixed-integer linear programming: a template-free approach

DOI10.1080/10556780600883742MaRDI QIDQ5758170zbMATH OpenOpenAlexFDO

Authors Scott R. McAllister, Rohit Rajgaria, Christodoulos A. Floudas

Publication date 3 September 2007

Published in Optimization Methods \& Software (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1080/10556780600883742

zbMATH Keywords

mixed-integer linear optimizationglobal pairwise sequence alignmentrank-ordered list of alignmentstheoretical guarantee

Mathematics Subject Classification ID

Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Mixed integer programming (90C11)

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Cites work

• Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

Cited in

(3)

• The mathematical model and optimistic algorithm of two protein structures alignment
• A path selection approach to global pairwise sequence alignment using integer linear optimization†
• An optimization approach to multiple sequence alignment

Describes a project that uses

Uses Software

• XPRESS
• CPLEX

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