ABOUT:

SIGRS (SIngle Genome ncRna Search) is a collection of routines used in searching for regions of contrasting composition 
(CCRs) in nucleotide sequences using a partial sum process.

Significance of segments is evaluated using Karlin-Altschul statistics and specifically an extension by 
Karlin-Dembo allowing for nucleotides to have a Markov-dependence (see e.g. 
http://www.pnas.org/cgi/reprint/90/12/5873 Karlin & Altschul (1993) and
http://www.jstor.org/view/00018678/ap050087/05a00070/0 Karlin & Dembo (1992)

The routines are provided as is and no guarantee regarding stability etc. is given. Hence, use at your own risk! 

See publication Larsson, P., Hinas, A., Ardell, D.H., Kirsebom, L.A., Virtanen, A. and Sderbom, F. 
"De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of 
Markov-dependent genome feature scoring" 
for details.

The latest version of SIGRS can be found at http://www.icm.uu.se/molbio/virtanen/publications/larsson_2008/supplemental/S4

Questions and comments can be directed to Pontus.Larsson@icm.uu.se

INSTALL:

The java and class files should be located in a directory named SIGRS. The SIGRS routines need
the external JAMA matrix package (v1.0.2) developed by MathWorks and NIST. It can be 
downloaded for free from http://math.nist.gov/javanumerics/jama/. Make sure the JAMA package is 
compiled and visible in your CLASSPATH.

Make sure that the directory where the SIGRS directory is located is in the CLASSPATH

Some documentation is available in the doc subdirectory

USAGE:

The SIGRS routines are invoked from the command line, e.g. 

	java -Xmx512M SIGRS.SIGRSMain -BG backgroundSequences.fa -TG targetSequences.fa -OUT M0_scores.txt
	
In this case, scores are calculated and written to M0_scores.txt. 512 MB of RAM is allocated to the JVM.
For a list of options, invoke the routines with the option -h

More exmples can be found in the example/ subdirectory

LICENSE:

SIGRS - Identifying genomic regions of contrasting composition using a partial sum process
Copyright  2008 Pontus Larsson

SIGRS is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

SIGRS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with SIGRS. If not, see http://www.gnu.org/licenses/ 
