A cost-aggregating integer linear program for motif finding

DOI10.1016/j.jda.2011.04.001zbMath1228.92026OpenAlexW2028931669WikidataQ39017930 ScholiaQ39017930MaRDI QIDQ655435

Mona Singh, Carl Kingsford, Elena Zaslavsky

Publication date: 4 January 2012

Published in: Journal of Discrete Algorithms (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jda.2011.04.001

zbMATH Keywords

computational biologysequence motif findings

Mathematics Subject Classification ID

Integer programming (90C10) Linear programming (90C05) Biochemistry, molecular biology (92C40) Algorithms in computer science (68W99) Algorithms on strings (68W32)

Cites Work

• Geometric algorithms and combinatorial optimization.
• Approximation algorithms for multiple sequence alignment
• Finding similar regions in many sequences
• A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies
• A Compact Mathematical Programming Formulation for DNA Motif Finding

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