The Institute for Systems Biology RMBlast Download

Overview
RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.

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.
Installation
Beginning with the 2.2.27+ release of BLAST+/RMBlast NCBI will be hosting the source and pre-compiled binaries for RMBlast. The BLAST+ source contains both packages in one distribution. The pre-compiled binaries are broken out into two distributions, the main BLAST+ toolkit and the new RMBlast application. If you choose to use the pre-compiled binaries you will need both for use with RepeatMasker/RepeatModeler.

  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-2.2.28:
    • cd /usr/local
    • tar zxvf ncbi-blast-2.2.28+-x64-linux.tar.gz
    • tar zxvf rmblast-2.2.28-x64-linux.tar.gz
    • cp -R rmblast-2.2.28/* ncbi-blast-2.2.28+/
    • rm -rf rmblast-2.2.28
    • mv ncbi-blast-2.2.28+ rmblast-2.2.28
  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.
To download and compile from the source code:
  1. Download RMBlast Source Packages:
    ncbi-blast-2.2.28+-src.tar.gz
    rmblast-2.2.28-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-2.2.28+-src.tar.gz
    • tar zxvf rmblast-2.2.28-src.tar.gz
  3. Build:
    To compile the programs for installation in /usr/local/rmblast run:
    • cd ncbi-blast-2.2.28+-src/c++
    • ./configure --with-mt --prefix=/usr/local/rmblast --without-debug
    • make
    • make install
    • cd ../..
    • cd rmblast-2.2.28-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.
Previous Version
rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
rmblast-1.2-ncbi-blast-2.2.23+-macos-intel.tar.gz
rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
Credits
 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
Release Notes
RMBlast 2.2.27+
  • First integrated release of NCBI BLAST+ toolkit and RMBlast.
RMBlast [1.2] NCBI Blast 2.2.23+
  • First release of RMBlast.
RMBlast is licensed under the Open Source License v2.1.
Institute for Systems Biology
This server is made possible by funding from the National Human Genome Research Institute (NIGRI grant # RO1 HG002939).