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NCBI BLAST for Windows Azure

Posted by Jonathan Allen on Dec 02, 2010

Sections: Operations & Infrastructure,; Architecture & Design,; Development
Topics: Windows Azure ,; Azure ,; .NET ,; PaaS ,; Programming ,; Cloud Computing ,; NCBI BLAST ,; Biotech

The full name of NCBI BLAST is the “Basic Local Alignment Search Tool of the National Center for Biotechnology Information”. NCBI BLAST was created by a group of researchers working for the National Institutes of Health, a division of the United States Department of Health and Human Services. NCBI describes BLAST as a tool that “finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.”

On November 16 Microsoft announced that NCBI BLAST is available on Windows Azure. In one demonstration they undertook a project for Seattle Children’s Hospital to examine the interrelationships of known protein sequences. It was claimed that for a single computer this analysis would have taken six years, but NCBI BLAST on Windows Azure completed the calculations in merely a week. (Note that the specifications for “one computer” option were not given. Clearly a single super-computer would be far faster than a single notebook computer.) In another demonstration they analyzed hydrogen production in bacteria for the University of Washington. According to Microsoft, “when Harwood Lab’s local resource was unable to handle the computation, the researchers submitted their request to a nationwide computer cluster, but the request was rejected after two days due to the long job-queuing time.” They go on to say that it took them only 3 days to complete the entire run on Windows Azure.

Windows Azure can run three different versions of BLAST, known as BlastP, BlastN, and BlastX. BlastP is used for searching protein databases for similar sequences. BlastN does the same thing for DNA sequences. BlastX is used to compare the conceptual translations of a DNA sequence against a protein sequence database. All three applications are run unaltered on Windows Azure. In addition a web role must be dedicated to the user interface and a worker role that divvies up the work amongst the individual instances of the BLAST application.

NCBI BLAST on Windows Azure is being offered at no cost to many researchers via Microsoft’s “Global Cloud Research Engagement Initiative”. This program is also known as the “Azure Research Engagement Project”.