ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. ScalaBLAST supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, or XML). ScalaBLAST will run on most multiprocessor systems that have MPI installed, and can run over a wide variety of interconnects including infiniband, quadrics, and ethernet. ScalaBLAST is designed to run a large number of queries against either large or small databases. ScalaBLAST parallelizes the BLAST calculations by dynamically scheduling them across processors using a fault-resilient scheme.
After downloading, untar the scalablast_source.tar.gz file, then follow the directions in the README for compiling and running ScalaBLAST.
The journal article describing ScalaBLAST is:
Oehmen, C.S. and J. Nieplocha. 2006. "ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis", IEEE Transactions on Parallel and Distributed Systems, 17(8): 740-749. ( Abstract is available on TPDS)
|Download Software||View Readme File|
|Version||v2.4.53||Requirements||gcc and MPI|
|Date Updated||August 12, 2013||File Size (Software Tool)||16 MB (.tar.gz)|
|Registration Required||No||File size (Readme)||5 KB (TXT)|
|Developers||C. Oehmen, D. Baxter, and J. Nieplocha|
All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:
This work was supported through the Laboratory Directed Research and Development at Pacific Northwest National Laboratory (PNNL), by the US Department of Energy's Office of Advanced Scientific Computing Research, and by the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.