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An Efficient Progressive Alignment Algorithm for Multiple Sequence Alignment


P.V.Lakshmi, Allam Appa Rao, GR Sridhar


Vol. 8  No. 10  pp. 301-305


Analyzing and comparing the string representations of sequences reveals a lot of useful information about the sequences. As new biological sequences are being generated at exponential rates, sequence comparison is becoming increasingly important to draw functional and evolutionary inference of proteins. This paper presents a partitioning approach for biomolecular sequence alignment that significantly improves the solution time and quality of the problem. The algorithm solves the multiple sequence alignment in three stages. First, an automated and suboptimal partitioning strategy is used to divide the set of sequences into several subsections. Then a multiple sequence alignment algorithm based on progressive method is used to align the sequences of each subsection. Finally, the alignment of original sequences can be obtained by assembling the result of each subsection. Test was conducted on two sets of sequences, namely BChE sequences of mammals and bacteria. Experimental results show that the algorithm can significantly reduce the running time and improve the solution quality of multiple sequence alignment


bioinformatics, multiple sequence alignment, partitioning, progressive alignment algorithm, biomolecular sequences