This year's problem for the MEMOCODE Design Contest is part of the DNA sequence alignment problem: exact substring matching. The challenge is to efficiently locate millions of 100-base-pair short read sequences in a 3-million-base-pair reference genome. Good solutions will combine judicious algorithm design with carefully designed data-handling architecture.

The 2012 MEMOCODE Design Contest is described here and its reference implementation there. The timeline for the design competition is as follows:

The conference will sponsor at least two prize categories, each with a significant monetary award (each of the two categories was awarded a $1000 prize in 2010). Each team delivering a complete and working entry will be invited to submit for review a 2-page abstract for the formal conference proceedings and present a poster at the conference. Winning teams will be invited to contribute a 4-page short paper and present their work at the conference.