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This paper presents a novel approach to solve the multiple sequence alignment (MSA) problem. the rubber band technique: index base (RBT-I) introduced in this paper, is inspired by the elastic behavior of a rubber band (RB) on a plate with poles. RBT-I is an iterative optimization algorithm designed and implemented to find the optimal alignment for a set of input protein sequences. In this technique, the alignment answer of the MSA problem is modeled as a RB, while the answer space is modeled as the plate with several poles resembling locations in the input sequences that are most likely to be correlated and/or biologically related. Fixing the head and tail of the RB at two corners of this plate, the RB is free to bend and finds its best configuration, yielding the best answer for the MSA problem. RBT-I is tested with one of the well-known benchmarks (BALiBASE 2.0) in this field. The obtained results show the superiority of the proposed technique even in the case of formidable sequences.
Date of Conference: March 31 2008-April 4 2008