Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Bioinformatics: Databases
           Computer: Demo Only

A DATABASE OF CODING SEQUENCES CONSERVATION BETWEEN RICE AND NONRICE CEREALS, AND ARABIDOPSIS

¹ Dept. of Plant and Microbial Biology, University of California, Berkeley, CA 94720

² C.N.R. Genomics Facility, University of California, Berkeley, CA 94720

We have established a searcheable database of coding sequences conservation between rice and nonrice cereals, and Arabidopsis at both the DNA and protein level. The database is built on data imported from NCBI UniGene database (http://www.ncbi.nlm.nih.gov/UniGene/) of the current UniGene datasets of three nonrice cereals (i. e., total in maize, 9897; in barley, 6965; in wheat, 12,467) and Arabidopsis (26,792). Blastx was used to compare these data with the rice protein database from GRAMENE (http://www.gramene.org/perl/protein_search), and blastn was used to compare these sequences against the rice indica genome sequences from BGI (http://btn.genomics.org.cn/rice/index.php). The results of the blast comparisons are stored in a SQL-based database, and a web interface was developed to aid in searching the data. Queries can be performed using various options, including species, percent identity, length of a match, sequence type (CDS or EST), or by key words. We believe this database is a useful resource for researchers to study of comparative genomics in grass family and plants, to clone genes using rice as reference, and other genomics studies.