UPIC

Principal Investigator(s):  View help for Principal Investigator(s) US Department of Agriculture; National Agricultural Library

Version:  View help for Version V1

Name File Type Size Last Modified
UPIC_v1.2.zip application/zip 229.3 KB 06/26/2026 11:45:AM
adc_metadata.json application/json 21.7 KB 06/26/2026 08:33:PM
catalog_detail.html text/html 9.3 KB 06/26/2026 11:45:AM

Project Citation: 

US Department of Agriculture, and National Agricultural Library. UPIC. Ann Arbor, MI: Inter-university Consortium for Political and Social Research [distributor], 2026-06-27. https://doi.org/10.3886/E250361V1

Project Description

Project Title:  View help for Project Title UPIC
Summary:  View help for Summary 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 (upic_optimum_v1.1.20101101.pl) 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: UPIC_v1.2.zip

Resource Title: UPIC version 1.2.

File Name: UPIC_v1.2.zip
Original Distribution URL:  View help for Original Distribution URL https://agdatacommons.nal.usda.gov/articles/model/UPIC/24664173

Scope of Project

Subject Terms:  View help for Subject Terms model; genotype; SSR/STR; DNA; Alleles; data.gov; ARS
Geographic Coverage:  View help for Geographic Coverage United States
Time Period(s):  View help for Time Period(s) 11/1/2010 – 11/1/2010
Collection Notes:  View help for Collection Notes DOI: 10.15482/USDA.ADC/1529201 Citation: Arias, Renee S.; Ballard, Linda L.; Scheffler, Brian E. (2019). UPIC. United States Department of Agriculture. https://doi.org/10.15482/USDA.ADC/1529201 (Downloaded 2026-06-26)


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Published Versions

V1 [2026-06-27]

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