RNApasta, v.1.01
================

Russell L. Malmberg* and Timothy I. Shaw**
*Plant Biology Department and Institute of Bioinformatics
**Institute of Bioinformatics
University of Georgia, Athens, GA 30602

Contact the author:
http://www.plantbio.uga.edu/~russell/?s=1&n=7&r=0

RNApasta is a java utility intended to work with RNA structural alignments, including the motifs of stem-loops and pseudoknots.  RNApasta can perform a variety of statistical analyses, and has editing capabilities intended to be useful with alignments that contain variable data such as the presence or absence of stem-loops or pseudoknots across sequences.  RNApasta can read Rfam-stockholm formatted files or pasta formatted files.

RNApasta is available compiled for Sun Java 1.6 or 1.5.  The source code is also available.  It has been successfully tested on Windows, Linux, and MacOS systems.

Additional information is in the Help.html file.

To Install:
===========
0.  The command "java -version" should tell you which java version you have installed.
1.  Download RNApasta-jar-1.6.zip or RNApasta-jar-1.5.zip as appropriate for your system.
2.  Unzip the zip file into a directory of your choice.
3.  The file RNApasta.jar is the executable program file.  The file list is given at the bottom.
For the MacOS bundle, read the ReadMe-Mac.txt file that accompanies it.

To Run:
=======
Use the files jar-start.bat (Windows) and jar-start.sh (Linux) to start the program from the RNApasta.jar file.  Click on one of these files or type the file name at the command line to start. With large data files, you might need to reserve more memory than the java default. The following line, which is used in jar-start, will start the file reserving 128 mb RAM:
  java -Xms128m -Xmx128m -classpath .\RNApasta.jar RpDefault.RNApasta

Start options:
jar-start.bat (Windows)  or  jar-start.sh (Linux)
   Starts the graphical interface.
jar-start infile
   Starts the graphical interface and loads the infile into the input text area.
jar-start infile outfile
   Bypasses the graphical interface; the infile is interpreted and saved in the outfile.
jar-start infile outfile integer
   Bypasses the graphical interface; the infile is analyzed according to the integer (see below) with results saved to the outfile.
   Command line integer options:
   jar-start infile outfile 1  	base frequencies
   jar-start infile outfile 2  	basepair frequencies by position
   jar-start infile outfile 3  	basepair frequencies by region
   jar-start infile outfile 4  	basepair frequencies by stem position
   jar-start infile outfile 5  	entropy by position
   jar-start infile outfile 6  	stack doublets
   jar-start infile outfile 7  	pseudofrequencies
   jar-start infile outfile 8  	frequencies of regions
   jar-start infile outfile 9  	stem summary
   jar-start infile outfile 10	loop summary
   jar-start infile outfile 0  	all of analyses 1-10

To Compile:
===========
If you need or wish to compile this yourself:
Download RNApasta.src.zip
Compile with this command or a similar one:
  javac -O -deprecation -verbose -Xlint:unchecked RpDefault/*.java
You can then start the program with:
  java -Xms128m -Xmx128m RpDefault.RNApasta
Or you can create a java archive (.jar file) and use that.
These commands are all given in several script files (.bat for windows, .sh for linux).

Files in zip package:
=====================
RNApasta.jar - executable, java archive
Help.html - help file
jar-start.bat - Windows command for starting the program
jar-start.sh - Linux command for starting the program
data - directory containing sample files
ReadMe-Win.txt - readme file with Windows line endings
ReadMe-Lin.txt - readme file with Linux line endings
Pasta.gif - icon file
Pasta.ico - icon file
Pasta.png - icon file
Pasta.xpm - icon file
Pasta.icns - icon file

Disclaimer: NO WARRANTY
=======================
This software was created in the course of academic and/or research endeavors and not as a commercial package. Its present version (which may still be in development) is distributed for a nominal fee to cover the cost of distribution and administrative costs, "AS IS, WITH ALL DEFECTS." By using the software, each user agrees to assume all responsibility for any and all such use. The author(s) and University of Georgia are not aware that the software or the use thereof infringe any proprietary right belonging to a third party. However, NO WARRANTY OR REPRESENTATION OF ANY KIND, EXPRESS OR IMPLIED, is made about the software, including without limitation any warranty of title, noninfringement, merchantability, or fitness for a particular purpose, by the author(s) or by University of Georgia.
Copyright 2009, Russell L. Malmberg, University of Georgia