FSA-BLAST is an improved clone of NCBI's popular BLAST tool. It was written by Michael Cameron. FSA stands for Faster Search Algorithm. FSA-BLAST is twice as fast as NCBI BLAST for large databases, with no loss of accuracy. These speed gains are due to a range of improvements to the BLAST algorithm .
Details at the FSA-BLAST web site.
- M. Cameron, H.E. Williams, and A. Cannane, Improved Gapped Alignment in BLAST, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1(3), 116-129, 2004.