MegaBLAST

MegaBLAST is a program for aligning sequences that differ slightly as a result of sequencing or other similar “errors”. When larger word size is used, it is up to 10 times faster than more common sequence-similarity programs. MegaBLAST is also able to efficiently handle much longer DNA sequences than the blastn program of the traditional BLAST algorithm. It uses the GREEDY algorithm for a nucleotide sequence alignment search.