Parallel Implementation of Centre Star Method in SMP Cluster for Multiple Sequence Alignment

Multiple Sequence Alignment is one of the most fundamental problems in computational molecular biology. The running time of the best known scheme for finding an optimal alignment, based on dynamic programming, increases exponentially with large number of input sequences. Hence, many approximation algorithms are suggested for the problem. Most of the bounded error approximation multiple sequence alignment algorithms developed for different objective functions use center star method which takes most of the overall running time in the above algorithms. Hence, there is a need to develop efficient parallel algorithm to speed up the solution of this time consuming problem. This paper presents a parallel centre star algorithm featuring a coarse grained parallelization approach. It is suitably implemented in SMP cluster using MPI library functions, which is the main architecture of current cluster systems. Results show that the proposed method offers an efficient way of getting the centre string to be used for large-scale multiple sequence alignment.