iMEC: Online Marker Efficiency Calculator

Premise of the Study To accurately design plant genetic studies, the information content of utilized markers and primers must be calculated. Plant genotyping studies should take into account the efficiency of each marker system by calculating different parameters to find the optimal combination of p...

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Bibliographic Details
Published inApplications in plant sciences Vol. 6; no. 6; pp. e01159 - n/a
Main Authors Amiryousefi, Ali, Hyvönen, Jaakko, Poczai, Péter
Format Journal Article
LanguageEnglish
Published United States John Wiley & Sons, Inc 01.06.2018
John Wiley and Sons Inc
Subjects
arbitrarily amplified dominant markers (AADs)
data collection
Deoxyribonucleic acid
DNA
DNA band
DNA fingerprinting
Efficiency
Genetic markers
Genotyping
Germplasm
Heterozygosity
Information processing
Internet
molecular marker
multi‐locus fingerprinting
Plant sciences
Polymorphism
Population
Primers
Software
Software Note
Software Notes
arbitrarily amplified dominant markers (AADs)
polymorphism
multi‐locus fingerprinting
molecular marker
DNA band
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Summary:Premise of the Study To accurately design plant genetic studies, the information content of utilized markers and primers must be calculated. Plant genotyping studies should take into account the efficiency of each marker system by calculating different parameters to find the optimal combination of primers. This can be problematic because there are currently no easily accessible applications that can be used to calculate multiple indices together. Methods and Results The program Online Marker Efficiency Calculator (iMEC) was developed using R for the simple computation of seven polymorphism indices (heterozygosity index, polymorphism information content, discriminating power, effective multiplex ratio, marker index, arithmetic mean heterozygosity, and resolving power). These indices are based on dominant and codominant DNA fingerprinting markers, thus allowing comparison and selection of optimal genetic markers for a given data set. Conclusions iMEC simplifies the calculation of diverse indices for the marker of choice to better enable researchers to measure polymorphism information for individual markers. The program is available at https://irscope.shinyapps.io/iMEC/.
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ISSN:2168-0450
2168-0450
DOI:10.1002/aps3.1159