Paracel's New Search Tool Makes Sequence Alignment a BLAST

Courtesy of Paracel

Researchers use BLAST to search previously characterized DNA or protein sequences for partial or total matches. For the last 12 years, Pasadena, Calif.-based Paracel http://www.paracel.com has been a major provider of clustered hardware and software used to perform these searches. Now the company offers a new release optimized for Paracel's latest 64-bit cluster hardware based on Advanced Micro Devices' (AMD's) Opteron processor.

"Unlike NCBI [National Center for Biotechnology Information] BLAST, Paracel BLAST is designed as a parallel application. Both can be run on clusters, but we can run a single job in parallel while NCBI can only run one job per processor," says Marc Raeffell, Paracel's senior manager of R&D.

Raeffell says Paracel BLAST can eliminate many of the bottlenecks in NCBI BLAST that cause problems with large sequences. "Typically NCBI gets slow at the 105 base range, and completely fails in the 106 to 107 range, ...