Computer Software to Find Genes in Plant Genomic DNA

Gene finding is the most important phase of genome annotation. Eukaryotic genomes contain thousands of protein coding genes, and computational gene prediction would rapidly increase the pace of experimental confirmation of expressed genes at the bench. The purpose of this chapter is to discuss the use of different computer programs that identify protein-coding genes in large genomic sequences. We describe most commonly used gene prediction programs that are available on the World Wide Web and demonstrate the use of some of these programs by an example. We provide a list of these programs along with their Web uniform resource locators (URLs) and suggest guidelines for successful gene finding.