Poster: Bioinformatics

Abs # 907: Construction of primer database using arabidopsis gene sequences

Presenter:	Lim, Yong Pyo , yplim@cnu.ac.kr
Authors	Lim, Yong Pyo  (A)   Hong, Chang Pyo  (A)   Park, Young Soo  (A)   Han, Jang Ho  (B)
Affiliations:	(A): Department of Horticulture and Genome Research Center, Chungnam National University, Daejeon, 305-764, Korea (B): Bioinformatics Division, National Institute of Agricultural Biotechnology, 225th, Seodun-dong Gwonseon-gu Suwon Gyeonggi-do, Korea

We constructed Atgene primer database (www.brassicagenome.org) based on ACEDB, having objected-oriented model and cross-referencing among genomic data, using module for parsing gene sequence and module for primer design of gene sequence applying high-throughput. The result generated the design for 129,885 primers against 26,828 genes. Atgene primer database have 6 classes containing chromosome, map, locus, gene name, primer, sequence. Especially, primer class contains the following contents; primer sequence, PCR product size, Tm value, GC contents, and the condition for 5 case of primer design. Now we have designed the primers for the partial mRNA, approximately 300-500bp, of Arabidopsis to use as the high-sensitivity probe as well as the universal primers for the conserved region among genes at a level of protein. This database may have the advantage of identifying genes, determining their functions, and especially, comparing for gene structure between Arabidopsis and Brassica.