:: Volume 3, Issue 1 (4-2012) ::
IJOR 2012, 3(1): 31-45 Back to browse issues page
An Application of the ABS LX Algorithm to Multiple Sequence Alignment
Lalwani , Kumar, Spedicato, Gupta
Abstract:   (15508 Views)
We present an application of ABS algorithms for multiple sequence alignment (MSA). The Markov decision process (MDP) based model leads to a linear programming problem (LPP), whose solution is linked to a suggested alignment. The important features of our work include the facility of alignment of multiple sequences simultaneously and no limit for the length of the sequences. Our goal here is to avoid the excessive computing time, needed by dynamic programming based algorithms for alignment of a large number of sequences. In an attempt to demonstrate the integration of the ABS approach with complex mathematical frameworks, we apply the ABS implicit LX algorithm to elucidate the LPP, constructed with the assistance of MDP. The MDP applied for MSA is a pragmatic approach and entails a scope for future work. Programming is done in the MATLAB environment
Keywords: Multiple sequence alignment, ABS algorithm, Dynamic programming, Markov decision process
Full-Text [PDF 332 kb]   (4089 Downloads)    
Type of Study: Original |
Received: 2011/06/8 | Accepted: 2013/06/22 | Published: 2013/06/22

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Volume 3, Issue 1 (4-2012) Back to browse issues page