q-gram Based DNA Database Searching Using a Suffix Array

our databases searching for similarity to a query sequence
has become a basic operation in molecular biology.
But even todays fast algorithms reach their limits when
applied to all-versus-all comparisons of large databases.
Here we present a new data base searching
algorithm dubbed QUASAR (Q-gram Alignment based on Suffix ARrays)
which was designed to quickly detect sequences with strong
similarity to the query in a context where many searches are
conducted on one database. Our algorithm applies a modification of
q-tuple filtering implemented on top of a suffix array. Two
versions were developed, one for a RAM resident suffix array and one
for access to the suffix array on disk. We compared our implementation
with BLAST and found that our approach is an order of magnitude faster.
It is, however, restricted to the search for strongly similar DNA
sequences as is typically required, e.g., in the context of clustering
expressed sequence tags (ESTs).