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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETICS, POPULATION DYNAMICS, AND MYCOTOXIN PREVENTION IN PEANUT

Location: Peanut Research

Title: Upic: Perl Scripts to Determine the Number of Ssr Markers to Run

Authors
item ARIAS DE ARES, RENEE
item BALLARD, LINDA
item SCHEFFLER, BRIAN

Submitted to: Meeting Proceedings
Publication Type: Other
Publication Acceptance Date: June 21, 2009
Publication Date: July 29, 2009
Citation: Arias, R.S., Ballard, L.L., Scheffler, B.E. 2009. UPIC: Perl scripts to determine the number of SSR markers to run. Molecular markers in Horticulture Symposium, July 29-31, 2009, Corvallis, Oregon State University. Meeting Proceedings.

Interpretive Summary: not required.

Technical Abstract: We have developed Perl Scripts for the cost-effective planning of fingerprinting and genotyping experiments. The UPIC scripts detect the best combination of polymorphic simple sequence repeat (SSR) markers and provide coefficients of the amount of information obtainable (number of alleles of patterns) for each combination of markers. In addition, the Perl Script package calculates polymorphic information content (PIC) values for various types of fertilization in organisms, and the percentage of heterozygous loci for each DNA sample. UPIC group of scripts is a very useful tool to plan experiments maximizing the information obtainable at the lowest cost.

Last Modified: 9/10/2014
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