The emerging area of metagenomics enables scientists to explore species diversity in challenging environments, such as ocean water at a particular longitude, latitude and depth; copper-mine runoff that measures pH 1; and the human gut.

In collaboration with a customer at The Salk Institute, TimeLogic provided access to an 8-card DeCypher system for analysis of the Global Ocean Survey sequence data. After one month of test searching and two weeks of continuous analysis time, over 30 million sequences were compared to a battery of protein classification databases (Pfam, TIGRfam, and Superfamily) using Hidden Markov Model analysis methods.

Reference:

Shibu Yooseph et al., The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families., PLoS Biology Vol. 5, No. 3, e16 doi:10.1371/journal.pbio.0050016.