Parallelisation of the blast algorithm.
Retrieving homologous DNA and protein sequences from existing databases is a fundamental routine in bioinformatics research. Programs of the NCBI BLAST family are widely used for this purpose. We evaluated paraBLAST, a parallelised version of the NCBI BLAST algorithm, using a Message Passing Interface (MPI) on a multi-node compute cluster. Here, we propose static and dynamic database-partitioning schemes based on the availability of the cluster. We evaluated the application of the algorithm in querying nucleotide sequences against a large-scale sequence database with different numbers of database partitions, and hence, different numbers of CPUs. Since the program's tasks are performed independently of each other, each available CPU can run its own copy of BLAST queries, resulting in reduced interference between processes and leading to a highly scalable solution.
Qi
Yutao
Y
BioInformatics Research Center, School of Computer Engineering Nanyang Technological University, Nanyang Avenue, Singapore 639798. antonioqi@pmail.ntu.edu.sg
Lin
Feng
F
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017385:Sequence Homology