Bio-blast is a project mainly written in Perl, it's free.
low-level routines for dealing with BLAST formats and data
Currently, this CPAN module only contains Bio::BLAST::Database.
Each object of Bio::BLAST::Database class represents an NCBI-formatted sequence database on disk, which is a set of files, the exact structure of which varies a bit with the type and size of the sequence set.
This is mostly an object-oriented wrapper for using fastacmd and formatdb to index sequence files and such.