title: UPIC: Perl scripts to determine the number of SSR markers to run.
abstract: We introduce here the concept of Unique Pattern Informative Combinations (UPIC), a decision tool for the cost-effective design of DNA fingerprinting/genotyping experiments using simple-sequence/tandem repeat (SSR/STR) markers. After the first screening of SSR-markers tested on a subset of DNA samples, the user can apply UPIC to find marker combinations that maximize the genetic information obtained by a minimum or desirable number of markers. This allows a cost-effective planning of future experiments. We have developed Perl scripts to calculate all possible subset combinations of SSR markers, and determine based on unique patterns or alleles, which combinations can discriminate among all DNA samples included in a test. This makes UPIC an essential tool for optimizing resources when working with microsatellites. An example using real data from eight markers and 12 genotypes shows that UPIC detected groups of as few as three markers sufficient to discriminate all 12- DNA samples. Should markers for future experiments be chosen based only on polymorphism-information content (PIC), the necessary number of markers for discrimination of all samples cannot be determined. We also show that choosing markers using UPIC, an informative combination of four markers can provide similar information as using a combination of six markers (23 vs. 25 patterns, respectively), granting a more efficient planning of experiments. Perl scripts with documentation are also included to calculate the percentage of heterozygous loci on the DNA samples tested and to calculate three PIC values depending on the type of fertilization and allele frequency of the organism.
  
  
  BACKGROUND
  Perl scripts are freely available for download from http://www.ars.usda.gov/msa/jwdsrc/gbru.
authors.affiliation: USDA/ARS Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd., Stoneville, MS 38776, USA.
authors.forename: Renee S
authors.initials: RS
authors.lastname: Arias
authors.forename: Linda L
authors.initials: LL
authors.lastname: Ballard
authors.forename: Brian E
authors.initials: BE
authors.lastname: Scheffler
references.citation: Am J Hum Genet. 1980 May;32(3):314-31
references.pmid: 6247908
references.citation: Theor Popul Biol. 2000 May;57(3):265-71
references.pmid: 10828218
references.citation: Mol Ecol. 2004 Jul;13(7):2101-6
references.pmid: 15189230
references.citation: Bioinformation. 2005 Nov 22;1(2):64-8
references.pmid: 17597856
references.citation: Microbiol Mol Biol Rev. 2008 Dec;72(4):686-727
references.pmid: 19052325
references.citation: Proc Natl Acad Sci U S A. 2007 May 15;104(20):8472-7
references.pmid: 17485665
references.citation: Genetics. 1974 Feb;76(2):379-90
references.pmid: 4822472
references.citation: Mol Ecol. 2002 Dec;11(12):2467-74
references.pmid: 12453232
references.citation: Mol Ecol. 1998 May;7(5):639-55
references.pmid: 9633105
references.citation: Trends Plant Sci. 2005 Dec;10(12):621-30
references.pmid: 16290213