中国科技论文在线

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2005年04月27日

【期刊论文】SilkDB: a knowledgebase for silkworm biology and genomics

王俊， Jing Wang， Qingyou Xia， Ximiao He，， Mingtao Dai， Jue Ruan， Jie Chen， Guo Yu， Haifeng Yuan， Yafeng Hu， Ruiqiang Li， Tao Feng， Chen Ye， Cheng Lu， Jun Wang， Songgang Li， Gane Ka-Shu Wong， Huanming Yang， Jian Wang， Zhonghuai Xiang， Zeyang Zhou and Jun Yu， *

Nucleic Acids Research, 2005, Vol. 33, Database issue D399-D402，-0001，（）：

-1年11月30日

摘要

The Silkworm Knowledgebase (SilkDB) is a webbased repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a 6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarina, a wild progenitor of B.mori, and a collection of genes from other Lepidoptera.Comparative analysis results between the domestic and wild silkworm, between B.mori and other Lepidoptera, and between B.mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies. SilkDB is publicly accessible at http://silkworm.genomics.org.cn.

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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

摘要

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

【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

摘要

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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2005年04月27日

【期刊论文】ChickVD: a sequence variation database for the chicken genome

王俊， Jing Wang， Ximiao He，， Jue Ruan， Mingtao Dai， Jie Chen， Yong Zhang， Yafeng Hu， Chen Ye， Shengting Li， Lijuan Cong， Lin Fang， Bin Liu， Songgang Li， Jian Wang， David W. Burt， Gane Ka-Shu Wong， Jun Yu， Huanming Yang， and Jun Wang， *

D438-D441 Nucleic Acids Research, 2005, Vol. 33, Database issue，-0001，（）：

-1年11月30日

摘要

Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DNA from domestic breeds. Using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNAsequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the 'Chicken Variation Database' (ChickVD). A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken. genomics.org.cn.

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2005年04月27日

【期刊论文】BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

王俊， Wenming Zhao， Jing Wang， Ximiao He， Xiaobing Huang， Yongzhi Jiao， Mingtao Dai， Shulin Wei， Jian Fu， Ye Chen， Xiaoyu Ren， Yong Zhang，， Peixiang Ni， Jianguo Zhang， Songgang Li， Jian Wang， Gane Ka-Shu Wong， Hongyu Zhao， Jun Yu， Huanming Yang and Jun Wang， *

Nucleic Acids Research, 2004, Vol. 32, Database issue D377-D382，-0001，（）：

-1年11月30日

摘要

Rice is a major food staple for the world's population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, we implemented our Rice Information System (BGIRIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis. In addition to comprehensive data from Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS also hosts carefully curated genome information from Oryza sativa L. ssp. japonica and EST sequences available from other cereal crops. In this resource, sequence contigs of indica (93-11) have been further assembled into Mbp-sized scaffolds and anchored onto the rice chromosomes referenced to physical/genetic markers, cDNAs and BAC-end sequences. We have annotated the rice genomes for gene content, repetitive elements, gene duplications (tandem and segmental) and single nucleotide polymorphisms between rice subspecies. Designed as a basic platform, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies (http://rise.genomics.org.cn/).

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