An Ant-Based Model for Multiple Sequence Alignment

Frédéric Guinand (1) , Yoann Pigné (1)

1 LITIS - Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes

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.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Intelligence artificielle [cs.AI]; Modélisation et simulation

Frédéric Guinand, Yoann Pigné. An Ant-Based Model for Multiple Sequence Alignment. Large-Scale Scientific Computing, 6th International Conference, LSSC 2007, Jun 2007, Sozopol, Bulgaria. pp.553-560, ⟨10.1007/978-3-540-78827-0_63⟩. ⟨hal-00264040⟩