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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS AND BIOINFORMATICS RESEARCH IN AGRICULTURALLY IMPORTANT ORGANISMS 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: Bioinformation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 11, 2009
Publication Date: April 21, 2009
Repository URL: http://parking.nal.usda.gov/shortterm/20388_UPIC_Bioinformation_2009.pdf
Citation: Arias, R.S., Ballard, L.L., Scheffler, B.E. 2009. UPIC: How Many SSR Markers to Run. Bioinformation 3(8):352-360, http://www.bioinformation.net/003/007800032009.htm

Interpretive Summary: Experiments of molecular fingerprinting (using DNA) can be very expensive specially if using large number of samples. Though the tools to identify and characterize specific DNA samples are available, we call them molecular markers, there were no tools to help decide how many of those hundreds of markers to use effectively. We developed a computer program called UPIC, can calculate how much information can be obtained with the least number of markers so the scientist can decide how many to use based on the size of his/her experiment and the available budget.

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: 12/18/2014
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