Fast distributed computing for complete large scale backtranslation of oligopeptides: Application to probe design

We present a new efficient distributed algorithm to compute a full backtranslation of short oligopeptides for functional microarrays, and to filter generated oligonucleotides according to usual selection criteria for the design of microarray probes. We used a model driven engineering and metaprogramming approach to simultaneously process several hundreds of oligopeptides whether using a PC, a multiprocessor server, a computing cluster or a computing grid. We implemented our algorithm with the C++ programming language and we present its performance and statistics on both simulated and real biological datasets. Our algorithm includes load balancing and the obtained results show a significant computing speedup on different architectures (SMP, cluster and Grid) and an important gain of about 40% of disk space when filtering oligonucleotides.