A New Heuristic for Multiple Sequence Alignment

Group Members: Rahna E, Shabana K M, M110113CS Vidya A S, Abstract:

Multiple sequence alignment is an important task in bioinformatics as it is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides. Several algorithms for multiple sequence alignment have been developed which are usually categorized into Progressive, Iterative, Divide and Conquer, etc. ClustalW is one of the most common and widely used progressive alignment approaches. It is a non-iterative, deterministic algorithm that attempts to optimize the weighted sums-of-pairs with affine gap penalties. It is a straightforward progressive alignment strategy where sequences are added one by one to the multiple alignment according to the order indicated by a pre-computed guide tree. Sequence addition is made using a pair-wise sequence alignment algorithm. However this method suffers from the drawback that its overall time complexity is O(N2n2) where N is the number of sequences to be aligned, each of length O(n). A heuristic has been proposed which reduces the overall time complexity to O(N (log2 N)n2). The heuristic proposed reduces the number of pair wise comparisons from O(N2) to O(N log2 N), and eliminates the need for constructing the guide tree, thereby reducing the time complexity.

References:
1. Ankit Agrawal, Siddhartha Kumar Khaitan, A new heuristic for multiple sequence alignment, IEEE 2008 2. C. Notredame, Recent progress in multiple sequence alignment: a survey, Pharmacogenomics, vol. 3,no. 1, pp. 131144, 2002. [Online] 3. J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucl. Acids Res., vol. 22, no. 22, pp. 46734680, 1994