NBLAST: A cluster variant of BLAST for NxN comparisons

Abstract

Background: The BLAST algorithm compares biological sequences to one another in order to determine shared motifs and common ancestry. However, the comparison of all non-redundant (NR) sequences against all other NR sequences is a computationally intensive task. We developed NBLAST as a cluster computer implementation of the BLAST family of sequence comparison programs for the purpose of generating pre-computed BLAST alignments and neighbour lists of NR sequences. Results: NBLAST performs the heuristic BLAST algorithm and generates an exhaustive database of alignments, but it only computes N(N-1)/2 alignments (i.e. the upper triangle) of a possible N2 alignments, where N is the set of all sequences to be compared. A task-partitioning algorithm allows for cluster computing across all cluster nodes and the NBLAST master process produces a BLAST sequence alignment database and a list of sequence neighbours for each sequence record. The resulting sequence alignment and neighbour databases are used to serve the SeqHound query system through a C/C++ and PERL Application Programming Interface (API). Conclusions: NBLAST offers a local alternative to the NCBI's remote Entrez system for precomputed BLAST alignments and neighbour queries. On our 216-processor 450 MHz PIII cluster, NBLAST requires ∼24 hrs to compute neighbours for 850000 proteins currently in the non-redundant protein database. © 2002 Dumontier and Hogue; licensee BioMed Central Ltd.