LAVA release 0.1


INTRODUCTION
------------

LAVA (LAMP Assay Versatile Analysis) is an extendable open-source Loop-mediated 
isothermal AMPlification (LAMP).  LAVA identifies combinations of six primer 
regions for basic LAMP signatures, or combinations of eight primer regions for 
LAMP signatures with loop primers, which can be used as LAMP signatures.  The 
identified primers are conserved among target organism sequences.  Primer 
combinations are optimized based on lengths, melting temperatures, and spacing 
among primer sites.

This is a Multiple-Sequence Alignment (MSA) approach to LAMP signature design.  
Either a single sequence or a pre-computed MSA can be used as input.  The 
individual sequences from the MSA are used for primer enumeration, with the goal 
of identifying as many locations for primers as possible.  Design parameters can 
be adjusted for each primer role.  Once primers have been identified that are 
shared among all the individual sequences, they are combined into potential 
inner primer pairs.  Finally, combinations of primers for the remaining roles of 
loop, middle, and outer, are analyzed to select LAMP signature candidates. 

The script slava.pl is also included as a demonstration of scaling to larger
genome sizes, but with this kind of implementation, the processing requirements
scale with the sequence size.  It's realistic to expect that a bacteria-sized
genome will take hours to days to execute, depending on the computing resources 
available.

SYSTEM REQUIREMENTS
-------------------

This is a Unix/Linux-only source code release.  It is not unreasonable to assume 
that the source code can be installed and run on other system types, with a 
minimal amount of effort spent porting, especially since it is primarily 
implemented in Perl.

Perl library XML::LibXML (available at http://www.cpan.org/)
	XML::LibXML is used for some of Options.pm's persistance capabilities

BioPerl 1.5.2 (available at http://www.bioperl.org/)
	BioPerl's fundamental utilities and file IO are used heavily
	
Primer3 1.0 (available at http://primer3.sourceforge.net/)
	Primer-selection code

Bio::Perl::Run (also available at http://www.bioperl.org/ as "bioperl-run")
	Bio::Perl::Run::Primer3 is used to execute system-level calls of Primer3


INSTALLATION INSTRUCTIONS
-------------------------

There are two components to this program, the script lava.pl, and the Perl 
modules that the script relies on.  Installation of the modules can be 
performed by entering the top-level directory of the distribution and running:

$ perl Makefile.PL
$ make
$ make test
$ make install

After the Perl modules are installed, the script lava.pl can be run from 
anywhere that the installed Perl modules are in the @INC path.


ACKNOWLEDGEMENTS
----------------	

This work was supported by a NIBIB Point-of-Care Technologies Research Network 
Center grant (Gerald J. Kost, PI of the UC Davis / LLNL POCT Center, 
NIH U54 EB007959). The content is solely the responsibility of the authors and 
does not necessarily represent the official views of the National Institute of 
Biomedical Imaging and Bioengineering or the National Institutes of Health.

This work performed under the auspices of the U.S. Department of Energy by 
Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.