IPM-HPC laboratory, defended its previous rank and won the Memocode design contest for the second time. The 2012 problem for the MEMOCODE Design Contest was part of the DNA sequence alignment problem: exact substring matching. The challenge was to efficiently locate millions of 100-base-pair short read sequences in a 3-million-base-pair reference genome.
IPM-HPC team provided two solutions: The first one is based on BWT data structure and the second one is based on Hash-indexing. Both of these methods use CPU-multicore and PThread technology. The Hash indexing method was one of the two winners of the contest. The method is able to align 1.2 GB of short read sequences in only 4 seconds. The hash-based solution become the winner of the normalized class of the contest. The hpc-team members of this year were: Aryan Arbabi,Milad Gholami, Mojtaba Varmazyar, Shervin Daneshpajouh. See details in the MEMOCODE page.