Researchers are deploying 'Roadrunner', the world fastest supercomputer, to analyse vast quantities of genetic sequences from HIV infected people in the hope of zeroing in on possible vaccine target areas.

Tanmoy Bhattacharya, physicist at Los Alamos National Lab, and HIV researcher Bette Korber have used samples taken by the Centre for HIV/AIDS Vaccine Immunology (CHAVI) from both chronic and acute HIV patients, worldwide.

They then created an evolutionary genetic family tree, known as a phylogenetic tree, to look for similarities in the acute versus chronic sequences that may identify areas where vaccines would be most effective.

'The petascale supercomputer gives us the capacity to look for similarities across whole populations of acute patients,' said Bhattacharya, who did his B.Sc and M.Sc in 1982 and 1984 from IIT-Kharagpur (India) and Ph.D. in physics from Tata Institute of Fundamental Research, Mumbai (India), in 1989.

'At this scale, we can begin to figure out the relationships between chronic and acute infections using statistics to determine the interconnecting branches - and it is these interconnections where a specially-designed vaccine might be most effective,' added Bhattacharya.

The study compared the evolutionary history of more than 10,000 sequences from more than 400 HIV-infected individuals.

The idea, according to Korber, is to identify common features of the transmitted virus, and attempt to create a vaccine that enables recognition of the original transmitted virus before the body's immune response causes the virus to react and mutate.

'DNA Sequencing technology, however, is currently being revolutionised, and we are at the cusp of being able to obtain more than 100,000 viral sequences from a single person,' said Korber, according to a Los Alamos release.

'For this new kind data to be useful, computational advances will have to keep pace with the experimental, and the current study begins to move us into this new era.'

On Memorial Day, May 26, 2008, 'Roadrunner' exceeded a sustained speed of one petaflop/s, or 1 million billion calculations per second. 'Petaflop' is computer jargon - peta signifying the number 1 followed by 15 zeros (sometimes called a quadrillion) and flop meaning 'floating point operation per second.'

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