An application of the ABS LX algorithm to multiple sequence alignement

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.

Il problema del multiple sequence alignement porta alla soluzione di sistemi lineari malcondizionati, per il cui trattamento si è usato con esiti positivi il metodo implicito LOX della classe ABS