
RMBLAST Release Notes 
   ( NCBI 2.2.28+ )

 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: www.phrap.org ) 
   - Support for cross_match-like masklevel filtering.
 
 Caveats
 =======
 Changes to the core ncbi algorithms were minimized and attempts were 
 made to shield the other standard NCBI programs included in this distrubtion
 from these changes.  However, we recommend that this package 
 be installed in a distinct directory from the standard NCBI 
 distribution on your system.  This will minimize the chance that
 packages other than RepeatMasker or RepeatModeler use this installation.
 This distribution is only intended for use with RepeatMasker/RepeatModeler.

 Credits
 =======
 Arian Smit - Institute for Systems Biology
 Robert Hubley <rhubley@systemsbiology.org>  - Institute for Systems Biology
 
 National Center for Biotechnology Information ( NCBI )
 
 And special thanks to:
   Tom Madden,
   Denis Vakatov,
   Aaron Ucko,
   Ning Ma, and
   George Coulouris 
 at 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

 Installation
 ============
 Binary Distribution:
   Download the binary distribution appropriate for your computer
   platform and extract the contents:

   % tar zxvf ncbi-blast-2.2.28+-x64-linux.tar.gz
  
   
 Source Distribution:
   Unpack the source distribution and run configure.  The following
   example configures rmblast for multi-threaded use ( required by
   RepeatMasker ), turns off debugging code generation, and sets
   the installation path to be /usr/local/rmblast.  NOTE: This will
   install the programs in /usr/local/rmblast/bin, /usr/local/rmblast/lib
   and so on:
  
    % tar zxvf rmblast-1.0-ncbi-blast-2.2.28+.tar.gz
    % cd rmblast-1.0-ncbi-blast-2.2.28+-src/c++/
    % ./configure --with-mt --prefix=/usr/local/rmblast --without-debug

   Build the programs:

    % make

   Install the programs:

    % make install


 Feedback
 ========
 Please visit www.repeatmasker.org to submit questions or feedback
 for us.
