This program will generate >4.0-fold (draft) DNA sequence coverage and approximately 10-fold clone coverage of the approximately 3 Gb rat genome within 18 months. 20 Mb of sequence will also be completed (finished) at high quality. The draft sequence will comprise approximately 65% whole genome shotgun reads, with the remainder from light coverage of 25,000 BACs. These sequences will be assembled and integrated with data from independent efforts that will produce both a fingerprint map, and BAC end-sequences (BES). The assembly will be accomplished by a suite of programs developed at the BCM-Human Genome Sequencing Center (BCM-HGSC). The data will be released immediately and annotated with all exact or near-exact matches using additional BCM-HGSC software. The eventual product will cover >90% of the euchromatic portion of the genome in contigs of 5-15 kb that are mostly ordered and oriented, and are confined to bins no greater than one BAC length. Finishing the rat sequence will be speeded by the development of a BAC minimum-tiling path across >95% of the genuine.
| Dewey, Colin; Wu, Jia Qian; Cawley, Simon et al. (2004) Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res 14:661-4 |
| Havlak, Paul; Chen, Rui; Durbin, K James et al. (2004) The Atlas genome assembly system. Genome Res 14:721-32 |
| Zhang, Zhengdong; Burch, Paula E; Cooney, Austin J et al. (2004) Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome. Genome Res 14:580-90 |
| Wu, Jia Qian; Shteynberg, David; Arumugam, Manimozhiyan et al. (2004) Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. Genome Res 14:665-71 |
| Dederich, Debra A; Okwuonu, Geoffrey; Garner, Toni et al. (2002) Glass bead purification of plasmid template DNA for high throughput sequencing of mammalian genomes. Nucleic Acids Res 30:e32 |
