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2005年04月27日
【期刊论文】RePS: A Sequence Assembler That Masks Exact Repeats Identified from the Shotgun Data
王俊， Jun Wang， ， Gane Ka-Shu Wong， Peixiang Ni， Yujun Han， Xiangang Huang， Jianguo Zhang， Chen Ye， Yong Zhang， Jianfei Hu， Kunlin Zhang， Xin Xu， Lijuan Cong， Hong Lu， Xide Ren， Xiaoyu Ren， Jun He， Lin Tao， Douglas A. Passey， Jian Wang， Huanming Yang， Jun Yu， and Songgang Li
，-0001，（）：
-1年11月30日
We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4
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2005年04月27日
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2005年04月27日
【期刊论文】Finishing the euchromatic sequence of the human genome
王俊
，-0001，（）：
-1年11月30日
The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers, 99% of the euchromatic genome and is accurate to an error rate of, 1event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.
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2005年04月27日
【期刊论文】A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms
王俊， Gane Ka-Shu Wong， ， *， Bin Liu*， Jun Wang， Yong Zhang， Xu Yang*， Zengjin Zhang， Qingshun Meng， Jun Zhou， Dawei Li， Jingjing Zhang， Peixiang Ni， Songgang Li， Longhua Ran， Heng Li， Jianguo Zhang， Ruiqiang Li， Shengting Li， Hongkun Zheng， Wei Lin， Guangyuan Li， Xiaoling Wang， Wenming Zhao， Jun Li， Chen Ye， Mingtao Dai， Jue Ruan， Yan Zhou， Yuanzhe Li， Ximiao He， Yunze Zhang， Jing Wang， Xiangang Huang， Wei Tong， Jie Chen， Jia Ye， Chen Chen， Ning Wei， Guoqing Li， Le Dong， Fengdi Lan， Yongqiao Sun， Zhenpeng Zhang， Zheng Yang， Yingpu Yu， Yanqing Huang， Dandan He， Yan Xi， Dong Wei， Qiuhui Qi， Wenjie Li， Jianping Shi， Miaoheng Wang， Fei Xie， Jianjun Wang， Xiaowei Zh
NATURE|VOL 432|9 DECEMBER 2004，-0001，（）：
-1年11月30日
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines-in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.
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