An Ant-Based Model for Multiple Sequence Alignment

DOI10.1007/978-3-540-78827-0_63MaRDI QIDQ3616857zbMATH OpenOpenAlexFDO

Authors Frédéric Guinand, Yoann Pigné

Publication date 26 March 2009

Published in Large-Scale Scientific Computing (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0803.2092

Mathematics Subject Classification ID

Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40)

Abstract: Multiple sequence alignment is a key process in today's biology, and finding a relevant alignment of several sequences is much more challenging than just optimizing some improbable evaluation functions. Our approach for addressing multiple sequence alignment focuses on the building of structures in a new graph model: the factor graph model. This model relies on block-based formulation of the original problem, formulation that seems to be one of the most suitable ways for capturing evolutionary aspects of alignment. The structures are implicitly built by a colony of ants laying down pheromones in the factor graphs, according to relations between blocks belonging to the different sequences.

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Cited in

(1)

• Multiple Sequence Alignment by Ant Colony Optimization and Divide-and-Conquer

Describes a project that uses

Uses Software

• ClustalW

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