It is much better to speed to aligment using heuristics (e.g. use hashing for find matching kmers and do dynamic programming only on small portion of data) than

It is much better to speed to aligment using heuristics (e.g. use hashing for find matching kmers and do dynamic programming only on small portion of data) than by using faster hardware. Look here: http://bowtie-bio.sourceforge.net/index.shtml http://bowtie-bio.sourceforge.net/index.shtml or here: http://mummer.sourceforge.net/ http://mummer.sourceforge.net/