January 15-19, 2005
Town & Country Convention Center
San Diego, CA
Ken Youens-Clark 1 , Kiran Kumar1 , Immanuel Yap2 , Pankaj Jaiswal2 , JunJian Ni2 , Steven Schmidt1 , William Spooner1 , Wei zhao1 , Liya Ren1 , Susan McCouch2 , Edward Buckler3, 4 , Lincoln Stein1 , Doreen Ware1,3
Due to the large size and complexity of many of the cereals genomes, finished genomic assemblies are unlikely to be available in the next few years. Many of these genomes will be represented by genomic sequences, ESTs, genetic and finger print contig physical maps. While these resources themselves are useful, it is often not possible to anchor many of the sequences to a physical location in their respective genomes. By leveraging the rice genome assembly, it is possible to order and orient many unanchored cereal sequenced based upon synteny in rice. These alignments will accelerate identification of genes using traditional mapped based cloning and the development of genetic and physical marker resources.
Gramene (http://www.gramene.org/), with support of funds from NSF and USDA, contributes to the development and implementation of bioinformatic resources for the plant community. One such resource, CMap, is a web-based comparative genetic and physical map tool that allows a user to dynamically generate comparative map views between the cereal genomes. Gramene implements the EnsEMBL genome browser, to display the rice assembly with anchored cereal annotations and a BLAST view. Both resources provide the users with interactive displays to link within the Gramene database and to act as a web-based portal to other genome resources. Over the next year we will be improving the CMap tool (available at http://www.gmod.org/) and supporting additional plant genome views in the EnsEMBL framework.