Bioinformatics and database of the rice genome

Abstract

After the completion of the genome sequencing of Asian cultivated rice (Oryza sativa ssp. japonica cv. Nipponbare) by the International Rice Genome Sequencing Project (IRGSP) (International Rice Genome Sequencing Project 2005), it was envisaged to decipher the underlying biological meanings of the genomic sequences. For this purpose, an indispensable step is to detect the locations of the genes and predict their precise exon-intron structures (Itoh 2007). This procedure is called gene-finding or gene prediction. Predicted genes will be the basis of further computational and experimental studies, such as molecular evolutionary analysis, transposon tagging and microarray experiments. In addition, databases are needed from which information about genome-wide analyses can be retrieved. In this chapter, we overview the bioinformatics methods and databases that are useful for data analysis of the rice genome.