"Wim Glassee" <wim.glassee@ua.ac.be> wrote on Fri, 7 Jun 2002: > the best. Cut the sequence into pieces, chop the database into pieces, > run them all against each other and merge the output. And as far as I > know this hasn't been done yet. According to Paracel, their version of Blast does exactly that: it fragments both the query sequence and the database, and the output -- including P and E values -- is identical to the output of NCBI Blast applied to the entire (non-fragmented) query sequence against the entire (non-fragmented) database. Ivo