This contains the Mitrion-C code for BLAST as well as a modified version of NCBI BLAST 2.2.13 for replacing the calculation core with calls to the FPGA.

mitc/blast-unrolled.mitc - The Mitrion implementation of stage 1 & 2 of BLAST
mitc/bloom/*             - VHDL Plugins for generating H3 Hash functions used 
                           by the blast mitrion code.
ncbi/                    - The patched NCBI blast source code.

Adjust the paths and the settings HOST_API and MODE in ./ncbi/make/mitrion-settings.inc to choose between rasclib or mithal and run ./ncbi/make/makedis.csh to compile.

If you have a valid Mitrion SDK with hardware generation, you can use the Mitrion SDK to generate a bitfile from the mitc source, register it under an algorithm name, for example 'blast'

> devmgr -a -n blast -b mitrion_xst.bin -c bitstream.cfg -s core_services.cfg

Build the BLAST host in mithal simulation mode and start a simulation server. Then run blast as usual. Note that the simulation is currently very slow, so you will probably not want to run a real query against a real database.

BLAST_FPGA_DEBUG=<0/1> - Set to 1 to enable debug messages

BLAST_BITSTREAM=<name> - the name of the bitstream to use. This should
                         be the same as was used to register the
                         bitstream. When running in the simulator,
                         this should be the name of the mitc source
                         file.

BLAST_FPGAS=<n> - The number of FPGA:s to scale the search
                  across. Set to 1 when running in the simulator.

RASCLIB_IO=<DIRECT/BUFFERED> - The I/O method rasclib should
                               use. (recommended: DIRECT). Only for
                               running in hardware.