Poster: Bioinformatics

Abs # 859: Construction of Database on Degenerate and Consensus (Hybrid) Primers for Brassica Genome Research

Presenter:	Lim, Yong Pyo , yplim@cnu.ac.kr
Authors	Lim, Yong Pyo  (A)   Hong, Chang Pyo  (A)   Park, Young Soo  (A)
Affiliations:	(A): Department of Horticulture, College of Agriculture, Chungnam National University

For making a framework for Brassica rapa L. spp. pekinensis genome sequencing such as comparative physical mapping and identifying homologous genes based in Brassica rapa on protein sequences of Arabidopsis, we are designing the Brassica degenerate and consensus (hybrid) primer database using conserved protein sequence regions among Arabidopsis, Brassica and other organisms, and developing its database. For designing degenerate primers, all known proteins of Arabidopsis were compared against NR protein database using BLASTP, and the sequences of hit proteins between Arabidoposis and Brassica were identified. We searched the conserved regions between these sequences using Block Maker (http://blocks.fhcrc.org/blockmkr/make_blocks.html), and designed the degenerate primers using CODEHOP (http://blocks.fhcrc.org/codehop.html). Currently, work is underway to design the degenerate primers against the known proteins on Arabidopsis chromosome 1. The results are being stored in a Brassica degenerate primer database using ACEDB. These primers will be available for making a framework for physical mapping, identifying proteins and developing InDel markers of Brassica.