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MASBioseq: a Multi-Agent System for Sequence Alignment with Dynamic Programming and R

This work presents an alternative to program sequence alignment algorithms with dynamic libraries. The work is based on Dynamic Programming techniques developed in C and R languages, alternatives of implementation and a comparison of their execution times. MASBioseq is a multi-agent platform that has been developed to allow distribution of data and to load balance of global and local sequence alignments according to Needleman-Wunsch and Smith-Waterman algorithms respectively. The new implementations provide with performance enhancements and an accessible graphical user interface to the researchers. The reason for developing this alternative is to check the performance improvement that can be obtained with the compilation of certain parts of the code in different languages, allowing a multiple and fast alignments.