Ag Data Commons
Browse (229.29 kB)


Download (229.29 kB)
posted on 2024-02-13, 13:42 authored by Renee S. Arias, Linda L. Ballard, Brian E. Scheffler

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.

The UPIC zip file contains 2 perl scripts, a README, and sample input and the resulting outputs. We would appreciate citation if you use them. As of 1 November, 2010, the zip file also contains an beta optimized script ( that produces a comma separated file, with all the markers that discriminate at least one line, which shows which lines have unique patterns. This allows you to select markers by score & line.

Resources in this dataset:

  • Resource Title: UPIC version 1.2.

    File Name:




Data contact name

Scheffler, Brian


United States Department of Agriculture

Temporal Extent Start Date



  • Not specified

Geographic Coverage


ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

cost effectiveness; DNA fingerprinting; genotyping; microsatellite repeats; screening; DNA; planning; alleles; heterozygosity; loci; computer software; models

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Arias, Renee S.; Ballard, Linda L.; Scheffler, Brian E. (2019). UPIC. United States Department of Agriculture.

Usage metrics



    Ref. manager