Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

GRAMA: Genetic Mapping Analysis Of Temperature Gradient Capillary Electrophoresis (TGCE) Data

Philip M. Maher¹ , Hui-Hsien Chou^1,2,3,4 , Elizabeth Hahn⁵ , Tsui-Jung Wen⁵ , Patrick S. Schnable^2,3,4,5

¹  Department of Computer Science, Iowa State University, Ames, IA 50011

²  L.H. Baker Center for Bioinformatics & Biological Statistics, Iowa State University, Ames, IA 50011

³  Center for Plant Genomics, Iowa State University, Ames, IA 50011

⁴  Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011

⁵  Department of Agronomy, Iowa State University, Ames, IA 50011

GRAMA, the Genetic Recombinant Analysis and Mapping Assistant, is a new tool that automates TGCE (Temperature Gradient Capillary Electrophoresis) data analysis for genetic mapping purposes. Data from multiple TGCE runs are integrated and displayed in an intuitive visual format. GRAMA includes its own algorithm to detect peaks in electropherograms, and peaks detected by GRAMA are automatically compared with those of another software package for any difference that will be flagged for user inspection. Analyses of the automatically combined genetic mapping results from GRAMA reveal high accuracy with virtually zero errors. Because of the accuracy of the calls and the intuitive interface, GRAMA boosts user productivity more than two-fold relative to previous manual methods in processing TGCE data and reduces errors. GRAMA is written in Java and can be freely downloaded from www.complex.iastate.edu.