LadderFinder
LadderFinder is a GPL program designed to solve a problem in DNA
genotyping. It helps in the construction of allelic ladders that drive the
sizing and
binning of SSR fragments produced by PCR. The algorithm scans a spreadsheet
containing a database of individual profiles and finds a minimum set of
individuals, that covers the maximum number of alleles represented in the
database, with all alleles represented only once.
The last constraint is imposed to make homogeneous the ladder peaks in the
pherograms. Given such a constrain, the best solution may not include all
alleles.
LadderFinder consists of two components:
a graphical interface and a program kernel.
The graphical interface is written in JAVA be portable, while the program kernel, called matchfinder, is written in C++ for efficency porpouse.
The graphical interface is written in JAVA be portable, while the program kernel, called matchfinder, is written in C++ for efficency porpouse.
The graphical interface uses both
JExcel and
Swing-Layout and
it allows to load an Excel/OpenOffice spreadsheet representing allele lengths
for each couple species/microsattelite.