Full Length Research Paper

A genome browser database for rice (Oryza sativa) and Chinese cabbage (Brassica rapa)

ChangKug Kim¹, JeomHwa Han², YounHee Shin¹, SungHan Park¹, DoWon Yun¹, ByungOhg Ahn³, DongHern Kim⁴, BeomSeok Park¹ and JangHo Hahn¹*

¹Genomics Division, National Academy of Agricultural Science (NAAS), Suwon 441-707, Korea.

²National Institute of Horticultural and Herbal Science (NIHHS), Naju 520-821, Korea.

³High-Tech Agriculture Division, Rural Development Administration (RDA), Korea.

⁴Bio-crop Division, National Academy of Agricultural Science (NAAS), Korea.

*Corresponding author. E -mail: jhhahn@rda.go.kr.

Accepted 18 September, 2009

   Abstract

We have constructed an integrated genome browser database for sequence analysis of rice (Oryza sativa) and Chinese cabbage (Brassica rapa) genomes. The genome browser for Arabidopsis (Arabidopsis thaliana) was included to provide the comparative analysis with Chinese cabbage. The genome browser of rice provides a variety of alternate views of the data in 12 chromosomes. Constructed from a supercontig using 3,360 BACs, it shows information about individual genes with functional annotation in the whole chromosome. In addition, the rice genome browser provides specific analysis of the genome by Gene Ontology (GO), single nucleotide polymorphisms (SNPs), Align, Text, Mart, BLAST and Export data views. In the comparative genome analysis between the Arabidopsis and Chinese cabbage genomes, users can obtain information using comparative genomics methods and identify missing regions within a single genome.

Key words: genome browser, Ensembl project, rice database, Chinese cabbage.