COPENHAGEN, July 23 - Compaq Computer and Edinburgh Biocomputing Systems said Monday they had successfully achieved one billion comparisons per second running the Smith-Waterman algorithm on a single 1 GHz Alpha processor.
In a demonstration at the International Conference on Intelligent Systems for Molecular Biology, EBS used its MPSRCH sequence analysis software to run a Smith-Waterman search on a 353-residue protein sequence in Swiss-Prot in 12.5 seconds. EBS CEO Shane Sturrock said the same search would have taken 17 times as long using a standard Smith-Waterman implementation such as S-Search on the same machine.
Sturrock said MPSRCH speed correlates directly with the clock speed of the computer it runs on, so the 1 GHZ capability of the Alpha processor enabled them to hit a billion comparisons per second for the first time.
Lionel Binns, worldwide life and materials science group manager for high-performance technical computing at Compaq, said the MPSRCH demo showed "how dependent advances in biology are on high-performance computing."
The 1 GHz Alphas will begin shipping in the fall. The EBS demo was the first public demonstration of live code on the 1 GHz machine, Binns said.
Noting that "there has been some confusion" in the life sciences community about the Alpha phase-out that the company announced several weeks ago, Binns reiterated that the company plans to support the Alpha technology even as it moves toward implementation of the Intel Itanium platform.Sturrock said that Compaq assured EBS that all code developed for the Alpha would work on future generations of the Itanium. He noted that MPSRCH will run on any 64-bit architecture, but EBS hasn't tested it on the Itanium yet.