GRAMA: genetic mapping analysis of temperature gradient capillary electrophoresis data |
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Authors: | Philip M. Maher Hui-Hsien Chou Elizabeth Hahn Tsui-Jung Wen Patrick S. Schnable |
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Affiliation: | (1) Department of Computer Science, Iowa State University, 503 Science II, Ames, IA 50011, USA;(2) L.H. Baker Center for Bioinformatics & Biological Statistics, Iowa State University, Ames, IA 50011, USA;(3) Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA;(4) Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA;(5) Department of Agronomy, Iowa State University, Ames, IA 50011, USA |
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Abstract: | Temperature gradient capillary electrophoresis (TGCE) is a high-throughput method to detect segregating single nucleotide polymorphisms and InDel polymorphisms in genetic mapping populations. Existing software that analyzes TGCE data was, however, designed for mutation analysis rather than genetic mapping. Genetic recombinant analysis and mapping assistant (GRAMA) is a new tool that automates TGCE data analysis for the purpose of genetic mapping. Data from multiple TGCE runs are analyzed, integrated, and displayed in an intuitive visual format. GRAMA includes an algorithm to detect peaks in electropherograms and can automatically compare its peak calls with those produced by another software package. Consequently, GRAMA provides highly accurate results with a low false positive rate of 5.9% and an even lower false negative rate of 1.3%. Because of its accuracy and intuitive interface, GRAMA boosts user productivity more than twofold relative to previous manual methods of scoring TGCE data. GRAMA is written in Java and is freely available at . |
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