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 http://www.complex.iastate.edu.
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Acknowledgments
We thank Dr. An-Ping Hsia for providing assistance in gathering materials and resources and editing the manuscript, Hsin “Debbie” Chen for early descriptions of the functionalities needed in a software program that was to become GRAMA, and Yi-Yin “Rita” Chen for entering much of the data from which our statistics were derived. We would also like to thank Sunyoung Park for her assistance in the creation of some of the figures and the other colleagues in the ISU Complex Computation Lab for discussion. This research was funded by National Science Foundation award DBI 0321711 to P.S.S. and others.
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Communicated by H. C. Becker
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Maher, P.M., Chou, HH., Hahn, E. et al. GRAMA: genetic mapping analysis of temperature gradient capillary electrophoresis data. Theor Appl Genet 113, 156–162 (2006). https://doi.org/10.1007/s00122-006-0282-6
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DOI: https://doi.org/10.1007/s00122-006-0282-6