The Institute for Systems Biology RMBlast Download

Overview
RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. 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

Latest Release: 2.9.0

We provide pre-built binaries of this version of RMBlast as a convenience to save users the expense of compiling RMBlast from source themselves. These distributions contain rmblastn and only the parts of BLAST+ that are used by RepeatModeler and RepeatMasker. They are not intended to be used as a general-purpose BLAST+ distribution.

We do not build binaries for all platforms. If your platform is unsupported or the binaries do not work on your machine, please compile RMBlast from source instead (instructions below).

To use the the pre-built binaries:
  1. Download Pre-compiled Package:
    Download the RMBlast package for your platform:
  2. Unpack RMBlast Distribution:
    Unpack the distribution in a place that will be accessible to RepeatMasker ( ie. /usr/local ).
    • cd /usr/local
    • tar zxvf rmblast-2.9.0-x64-linux.tar.gz
  3. Configure RepeatMasker/RepeatModeler:
    To use the new search engine with RepeatMasker or RepeatModeler, run/re-run the configure program in the RepeatMasker directory and the configure program in the RepeatModeler directory.
To compile from source:
  1. Download NCBI Blast+ and rmblast patch file:
    ncbi-blast-2.9.0+-src.tar.gz
    isb-2.9.0+-rmblast.patch.gz
  2. Install Dependencies:
    You will need a C++ compiler and essential build tools such as make and autotools.
    • Debian and derivatives (Ubuntu, Mint, etc.): apt install build-essential
    • Fedora: yum groupinstall "Development Tools"
    Other missing dependencies might be detected by the configure step later, depending on your operating system.
  3. Unpack Distribution:
    Unpack the distribution in your home directory or in a temporary location ( i.e. /tmp ).
    • cd /mytmp/location/
    • tar zxvf ncbi-blast-2.9.0+-src.tar.gz
    • gunzip isb-2.9.0+-rmblast.patch.gz
  4. Patch:
    • cd ncbi-blast-2.9.0+-src
    • patch -p1 < ../isb-2.9.0+-rmblast.patch
  5. Build:
    To compile the programs for installation in /usr/local/rmblast run:
    • cd ncbi-blast-2.9.0+-src/c++
    • ./configure --with-mt --without-debug --without-krb5 --without-openssl --with-projects=scripts/projects/rmblastn/project.lst --prefix=/usr/local/rmblast
    • make
      • make -j can be used to parallelize the build on multiprocessor systems, e.g. make -j2 to dedicate two cores to the build process.
    • make install
  6. Configure RepeatMasker/RepeatModeler:
    To use the new search engine with RepeatMasker or RepeatModeler, run/re-run the configure program in the RepeatMasker directory and the configure program in the RepeatModeler directory.

Previous Release: 2.6.0 ( ver 2 )

The previous release of rmblast ( 2.6.0 ) is currently only available as a patch to the source distribution from NCBI.

  1. Download RMBlast Source Package and Patch File:
    ncbi-blast-2.6.0+-src.tar.gz
    isb-2.6.0+-changes-vers2.patch.gz ( updated 3/29/17 - bugfix )
  2. Unpack Distribution:
    Unpack the distribution in your home directory or in a temporary location ( ie. /tmp ).
    • cd /mytmp/location/
    • tar zxvf ncbi-blast-2.6.0+-src.tar.gz
    • gunzip isb-2.6.0+-changes-vers2.patch.gz
  3. Patch:
    • cd ncbi-blast-2.6.0+-src
    • patch -p1 < ../isb-2.6.0+-changes-vers2.patch
  4. Build:
    To compile the programs for installation in /usr/local/rmblast run:
    • cd ncbi-blast-2.6.0+-src/c++
    • ./configure --with-mt --prefix=/usr/local/rmblast --without-debug
    • make
    • make install
  5. Configure RepeatMasker:
    To use the new search engine with RepeatMasker or RepeatModeler, run/re-run the configure program in the RepeatMasker directory followed by the configure program in the RepeatModeler directory.
 Arian Smit - Institute for Systems Biology
 Robert Hubley   - Institute for Systems Biology
 Jeb Rosen  - Institute for Systems Biology
 
 National Center for Biotechnology Information ( NCBI )
 
 And special thanks to:
   Tom Madden,
   Christiam Camacho,
   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 2.9.0+
  • Updated to current NCBI release.
  • Provide pre-compiled RMBlast and BLAST+ binaries for RepeatMasker and RepeatModeler.
RMBlast 2.6.0+
  • Updated to current NCBI release.
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).