Anchoring of rice BAC clones to the rice genetic map in silico

A wealth of molecular resources have been developed for rice genomics, incl uding dense genetic maps, expressed sequence tags (ESTs), yeast artificial chromosome maps, bacterial artificial chromosome (BBC) libraries and BAC en d sequence databases, Integration of genetic and physical maps involves lab or-intensive empirical experiments. To accelerate the integration of the ba cterial clone resources with the genetic map for the International Rice Gen ome Sequencing Project, we cleaned and filtered the available EST and BAC e nd sequences for repetitive sequences and then searched all available rice genetic markers with our filtered databases. We identified 418 genetic mark ers that aligned with at least one BBC-end sequence with >95% sequence iden tity, providing a set of large insert clones with an average separation of 1 Mb that can serve as nucleation points for the: sequencing phase of the I nternational Rice-Genome Sequencing Project.