RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include:

• Support for custom matrices ( without KA-Statistics ).
• Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
• Support for cross_match-like masklevel filtering.

1. Download Pre-compiled Package:
   Download both the BLAST+ and RMBlast packages from NCBI for your platform:
   RMBlast Binaries:ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/LATEST
   BLAST+ Binaries:ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
   
2. Unpack BLAST+ Distribution:
   Unpack the distributions in a place that will be accessible to RepeatMasker ( ie. /usr/local ). Note both distributions will end up in the same directory called rmblast-2.2.27:
   • cd /usr/local
   • tar zxvf ncbi-blast-2.2.27+-x64-linux.tar.gz
   • tar zxvf rmblast-2.2.27-x64-linux.tar.gz
   • cp -R rmblast-2.2.27/* ncbi-blast-2.2.27+/
   • rm -rf rmblast-2.2.27
   • mv ncbi-blast-2.2.27+ rmblast-2.2.27
3. Configure RepeatMasker:
   To use the new search engine with RepeatMasker, run/re-run the configure program in the RepeatMasker directory. NOTE: RepeatMasker open-3.2.9 or higher is required to use RMBlast.

1. Download RMBlast Source Packages:
   ncbi-blast-2.2.27+-src.tar.gz
   rmblast-2.2.27-src.tar.gz
2. Unpack Distribution:
   Unpack the distribution in your home directory or in a temporary location ( ie. /tmp ).
   • cd /mytmp/location/
   • tar zxvf ncbi-blast-2.2.27+-src.tar.gz
   • tar zxvf rmblast-2.2.27-src.tar.gz
3. Build:
   To compile the programs for installation in /usr/local/rmblast run:
   • cd ncbi-blast-2.2.27+-src/c++
   • ./configure --with-mt --prefix=/usr/local/rmblast --without-debug
   • make
   • make install
   • cd ../..
   • cd rmblast-2.2.27-src/c++
   • ./configure --with-mt --prefix=/usr/local/rmblast --without-debug
   • make
   • make install
4. Configure RepeatMasker:
   To use the new search engine with RepeatMasker, run/re-run the configure program in the RepeatMasker directory. NOTE: RepeatMasker open-3.2.9 or higher is required to use RMBlast.

 Arian Smit - Institute for Systems Biology
 Robert Hubley   - Institute for Systems Biology
 
 National Center for Biotechnology Information ( NCBI )
 
 And special thanks to:
   Tom Madden,
   George Coulouris,
   Denis Vakatov,
   Aaron Ucko,
   Ning Ma
 from NCBI for allowing me to bug them with questions about
 the BLAST source code, assistance with finding resources,
 and lending an ear to a tired programmer.

 This work is funded by NHGRI grant # RO1 HG002939-07

• First integrated release of NCBI BLAST+ toolkit and RMBlast.

• First release of RMBlast.