GRAMA: genetic mapping analysis of temperature gradient capillary electrophoresis data.
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 .
Maher
Philip M
PM
Department of Computer Science, Iowa State University, 503 Science II, Ames, IA 50011, USA.
Chou
Hui-Hsien
HH
Hahn
Elizabeth
E
Wen
Tsui-Jung
TJ
Schnable
Patrick S
PS
D000465:Algorithms; D002874:Chromosome Mapping / Q000706:statistics & numerical data*; D003627:Data Interpretation, Statistical; D019075:Electrophoresis, Capillary / Q000706:statistics & numerical data*; D007178:Inbreeding; D012984:Software; D013696:Temperature; D003313:Zea mays / Q000235:genetics