Title : Analysis of High-Speed Multiple Sequence Alingment of Amino Acids

Group Members :

• Ankush Dharkar

Abstract :

The world has turned towards parallel & distributed computing over the last few years to solve difficult problems of time and space complexity. Why shouldn't bioinformatics also use it to get its work done, rather than wait for better sequential algoritms,if any, to get devised?

My project also aims to use them to come up with a parallel algorithm for doing multiple sequence alingment and finding motifs. The project will also take into consideration the BLOSUM matrix for degeneracy in the protein sequences. It will also try to evaluate the extent of effects of mutation in proteins on these motifs

Plan of Action :

• Devise a parallel algorithm and architecture for the experiments
• Code the framework required for the experiments
• Collect proteins from PDB and run experiments
• Tally the correctness of the algorithm
• Plot the graphs for statistics and generate reports
• Induce mutation and evaluate the effects on the motifs

Factors of Success :

• Lowering of the Complexities in solving problems
• Speed-Ups in time attained
• Analysis of the degeneracy and mutation factors, and how they affect the motifs