PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of seed" words (typically 11-12 bases) as well as an index of the precomputed scores of short words (typically 7-8 bases) aligned against each other.