FindingGenesintheRiceGenome.pptVIP

Finding Genes in theRice Genome Hao Bailin T-Life Research Center, Fudan University Beijing Genomics Institute , Academia Sinica Institute of Theoretical Physics, Academia Sinica (/~hao/) On-going work by a team of 10-12 people since August 2001: Zheng Weimou, Xie Huimin, Liu Jinsong, Xu Zhao, Fang Lin, Li Heng, Gao Lei, Jin Jiao, et al. Nothing written yet. Two Cultivars of Rice Oryza sativa ssp. indica (籼稻) Oryza sativa ssp. Japonica (粳稻) The difference was described in Xu Shen’s (许慎《说文解字》) Chinese Dictionary of East Han Dynasty (~ 2nd Century AD) J.H. Zhang et al. Rice cultivation of Jianhu Remains in Henan Province, Science J. (《科学》杂志)，53（4），2002， 3 (in Chinese) Gene-Finding by Computer Starting from early 1980s: “Ab initio” or “de novo” algorithms: GeneMark, GenScan, FgeneSH, Genie, …based on gene-structure models and training data. (Our on-going project: BGF, the BGI Gene Finder) Homolog methods based on sequence alignment with known genes in databases Mixed approach using both strategy: TwinScan Different Stages of Gene-Finding Use all possible existing programs and services on the web with a public-domain or home-made genome viewer Write your own gene-finder, trained for the specific organism A dream for the time being: design a self-training and self-developing program “for any species” which would improve itself iteratively starting from a few available reads, cDNAs, and ESTs Performance of Gene-Finders in Eukaryote Genomes M. Q. Zhang, Nature Review Genetics, 3 (2002) 698-710 (mostly for the human genome): Nucleotide level: 80% Exon level: 45% Whole gene structure: 20% FgeneSH and BGF for rice (our tests on 128 cDNA-confirmed single-gene genomic sequences): Nucleotide level: 90% Exon level: 60% Whole gene structure: 40% Three Scales of Search Local: signals with minimal signature (start, stop, splicing); movable signals (caps, promoters, polyAs, branching points, some very weak) --- cl