Logical Depth

The Sargasso Sea
245K sequences
7700 HMMs
5 hours

" LDhmmer is working well on our cluster and multiple TIGR researchers have mentioned to me that they have noticed marked improvement in the speed of their HMM searches.

A large search for the Sargasso Sea* was 245,000 sequences against 7700 HMM profiles. If you define an HMM search as a single sequence against a single profile that's roughly 2 billion searches.

We thought the search may take a couple days but it finished in less than 5 hours on our cluster giving a performance of about 6 million searches per minute.

Other searches were running at equal priority so that's a lower bound for LDhmmer performance. "

— Dan Sommer, TIGR

* Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., Fouts, D.E., Levy, S., Knap, A.H., Lomas, M.W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y.H. and Smith, H.O. (2004). Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science 2004 Apr 2;304(5667):66-74.

Fast.

The Sargasso Sea 245K sequences 7700 HMMs 5 hours

The Sargasso Sea
245K sequences
7700 HMMs
5 hours