AbstractsComputer Science

A user friendly environment for gene-finding program evaluation (GFPE)

by Weicheng Zhang

Institution: University of Georgia
Department: Computer Science
Degree: MS
Year: 2003
Keywords: Gene-Finding Program Evaluation
Record ID: 1733974
Full text PDF: http://purl.galileo.usg.edu/uga_etd/zhang_weicheng_200308_ms


A graphical, user friendly environment for GFPE (Gene-Finding Program Evaluation), written in Java, is developed to evaluate the prediction accuracy of gene-finding programs GenScan, HMMGene, GeneMark, Pombe and FFG. This tool aims to simplify and/or automate the process of executing the gene-finding programs on sequences of interest and of collecting and analyzing the results. The GUI is designed to be similar to a spreadsheet table. The user can add, cut, copy or paste gene sequence files and annotation files to the table, add, delete, or modify the GFPE program and parameters, select an area on the table to represent the execution of various gene-finding programs on remote servers, automatically collect the prediction results, and draw bar charts to compare evaluation accuracy at the coding level, exon level and protein level. It provides a convenient, user-friendly environment and an efficient file management and execution system, thus saving the user substantial time.