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.
Caveats
Changes to the core algorithms were minimized and attempts were made to shield the standard NCBI programs included in this distrubtion from these changes. However, it is recommended that this package be installed in a different directory from the standard NCBI distribution so as to minimize the chance other packages will attempt to call blastn, blastp..etc from this installation. This distribution is only intended for use with RepeatMasker/RepeatModeler.
Installation
If you have a linux x64 based system or MacOSX Intel you can download pre-compiled versions of RMBlast:
  1. Download Pre-compiled versions:
    rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
    rmblast-1.2-ncbi-blast-2.2.23+-macos-intel.tar.gz
  2. Unpack Distribution:
    Unpack the distribution in a place that will be accessible to RepeatMasker ( ie. /usr/local ).
    • cd /usr/local
    • tar zxvf rmblast-1.2-ncbi-blast-2.2.23+-x64-linux.tar.gz
  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:
    rmblast-1.2-ncbi-blast-2.2.23+-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 rmblast-1.2-ncbi-blast-2.2.23+-src.tar.gz
  3. Build:
    To compile the programs for installation in /usr/local/rmblast run:
    • cd rmblast-1.0-ncbi-blast-2.2.23+-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.
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,
   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
Release Notes
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 HG002939-01) 2003.