系统发育信息学及网络资源

系统发育信息学是近年来形成的新的学科方向,是系统学研究领域的一个新兴生长点。系统发育信息学是存贮、管理、注释、开发和加工系统树及其相关生物学信息的交叉学科。它的方法是基于计算机和网络技术,包括大型系统树及其相关生物学数据库的建立,系统树数据库网络的构架,系统树的可视化显示,小系统树的联合与超树的建立、用户查询、搜索和下载等,最终目的是要建立一个囊括地球上所有生物的系统树及其相关信息的数据库,将各种生物在树上精确定位,并进一步通过对系统发育信息的查询、搜索、联合与分析,从中获取生命进化的知识和进行生物学的预测。目前可用的系统发育网络资源主要有CIPRes和系统发育软件(PhylogenyPrograms)网站,已建立的系统发育信息学数据库包括TreeBASE,TreeofLife,Species2000,NCBITaxonomy数据库等。     

宏蛋白质组学信息分析的基本策略及其挑战

宏蛋白质组学是一门新型科学,它运用质谱技术规模化地采集自然界微生物种群的蛋白质信息,并结合多种组学数据,开展微生物种群的遗传特征及其生物功能的研究.宏蛋白质组学的信息分析与传统蛋白质组学方法有较大的不同,亟需拓展新的分析思路.由于宏蛋白质组的研究对象是复杂度极高的微生物样品,因此,需要构建尽可能囊括样本中所含微生物的基因组信息的物种数据库.面对庞大的数据库,必须考虑到分析过程中所消耗的计算资源和鉴定结果的质控标准,因此,需要高度优化库容量、搜库、假阳性控制等参数.鉴于宏蛋白质组数据中广泛存在复杂的同源蛋白质序列,因此,需要充分利用NCBI数据库中的分类信息进行匹配,并运用LCA算法过滤处理才能将蛋白质有效地归组到物种.本文立足于宏蛋白质组学信息分析,从宏蛋白质组的数据库建立、蛋白质归并、生物学意义发掘等几个方面着手,对该领域的发展现状、面临挑战以及未来研究方向进行了评述.     

上海农作物种质资源数据库的设计和构建

随着农作物种质资源数量的不断增加,种质资源交流的日益频繁以及种质资源利用的逐步深入,农作物种质资源数据库的建设对农作物的应用研究和基础性研究至关重要。上海市农业生物基因中心借助于本中心保存的近21万份种质资源的信息,开发了一套上海农作物种质资源数据库,本文主要阐述了该数据库设计和构建的目的、原则和数据库的架构、运行环境以及主要功能模块。上海农作物种质资源数据库采用了B/S结构,平台系统利用多层逻辑架构实现了对农作物种质资源数据信息的收集、存储、查询、统计分析等功能。外部用户通过浏览器即可访问平台系统,浏览查询种质资源信息。内部管理员可使用平台的受限功能,需要认证成功后才可使用后台管理功能,实现对整个平台数据的管理。注册用户还可通过基因资源数据库提交引种申请,管理员结合管理信息系统实现对外供种全流程的网络化,借此可提高工作效率,增加工作流程的透明度。     

园艺植物分子育种相关生物信息资源及其应用

园艺植物分子育种中, 生物信息技术是一项新技术。GenBank、EMBL、DDBJ、Swiss-Prot等数据库及其序列查询系统、序列比对软件和序列提交软件是园艺植物分子育种中的重要生物信息资源。本文综述了这些生物信息资源, 以及它们在克隆新基因、预测新序列功能、鉴定种质资源和进行系谱分析等方面的应用。     

园艺植物分子育种相关生物信息资源及其应用

园艺植物分子育种中,生物信息技术是一项新技术.GenBank、EMBL、DDBJ、Swiss-Prot等数据库及其序列查询系统、序列比对软件和序列提交软件是园艺植物分子育种中的重要生物信息资源.本文综述了这些生物信息资源,以及它们在克隆新基因、预测新序列功能、鉴定种质资源和进行系谱分析等方面的应用.     

NCBI高通量测序数据库SRA介绍

随着新一代测序技术的发展,高通量测序技术的应用越来越广泛,其产生的海量数据的存储、查询需要专门的数据库辅助,NCBI的SRA(Sequence Read Archive)数据库是高通量测序存储的代表,本文对SRA数据库的组织架构,数据形态作了综述分析,并对其存贮的数据进行了总结。     

基于基因本体论的生物信息个人数据库平台

论述了一个基于基因本体论(geneontology)的生物信息个人数据库平台BIO.该数据库平台根据自身研究的需要,用基因本体论中的相关的规范术语来对基因序列信息进行注释,从而可以让用户从基因本体论的角度对生物信息序列进行查询.由于因特网上生物数据库中大量的关于基因序列信息的术语不统一、不规范,存在大量的信息冗余,用此方式可最大限度地精确所要查找的结果.文中详细论述了该数据库平台的研究背景、查询功能以及维护.     

民族药用植物指纹数据库的构建研究

通过对四川省时采集的民族药用植物标本进行基因和化学指纹图谱、药用价值、民族传统利用等信息的整理,用SQL Server 2000建立一个民族药用植物指纹的开放式关系数据库初步框架。该数据库重点体现药用植物的民族利用特色,同时包括各种指纹图谱图片。该数据库不仅可以快速、方便地检索和查询有关民族药用植物的背景资料、药用价值以及指纹图谱信息,而且可为四川省内民族药用植物资源的保护和利用提供基础。     

乳腺癌基因芯片数据使用探讨

随着生命科学的迅猛发展,生物信息量的急剧增加,大量基因芯片的实验数据是公开发布在Internet网上的,尤其是学术机构在发表论文时所使用的实验数据都可以免费提供给研究人员下载使用。如何能有效地、正确地利用这些数据资源,特别是在利用数据验证算法、训练模型等问题的研究中,查询和使用基因芯片数据库网上资源便显得非常重要。对与乳腺癌基因芯片有关的数据库的数据查询及使用进行研究和探讨。     

秦岭种子植物数据库信息系统的结构和功能简介

秦岭种子植物数据库已经建成,本文简介了建库目标,系统结构和功能,本库对秦岭种子植物１６９科１０１０属３０２８种按基本信息,名称,分布和用途等设计了方便的检索查询系统,对它在秦岭植物资源开发,利用和保护以及生物多样性,区系研究等方面的应用也做了讨论。     

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval and resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing pages, GeneMap'99, Davis Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP) pages, Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP) pages, SAGEmap, Online Mendelian Inheritance in Man (OMIM) and the Molecular Modeling Database (MMDB). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov     

Database resources of the National Center for Biotechnology Information: 2002 update

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI’s web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, Human¡VMouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.     

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap'99, Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri-tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov.     

Database resources of the National Center for Biotechnology

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.     

A real-time and dynamic biological information retrieval and analysis system (BIRAS)

The aim of this study is to design a biological information retrieval and analysis system (BIRAS) based on the Internet. Using the specific network protocol, BIRAS system could send and receive information from the Entrez search and retrieval system maintained by National Center for Biotechnology Information (NCBI) in USA. The literatures, nucleotide sequence, protein sequences, and other resources according to the user-defined term could then be retrieved and sent to the user by pop up message or by E-mail informing automatically using BIRAS system. All the information retrieving and analyzing processes are done in real-time. As a robust system for intelligently and dynamically retrieving and analyzing on the user-defined information, it is believed that BIRAS would be extensively used to retrieve specific information from large amount of biological databases in now days. The program is available on request from the corresponding author.     

植物激素相关核酸和蛋白质二级数据库的构建与应用

以NCBI维护的一级数据库为数据源建立植物激素相关核酸和蛋白质二级数据库。将该二级数据库设计为基因、蛋白质和文献三部分, 编写软件从上述数据源中采集数据, 并以XML作为中间格式保存, 通过解析提交到二级数据库中并集成部分生物信息学工具软件, 初步实现了数据检索、统计分析、基于Web的本地化BLAST同源序列检索、序列的自动拼接以及蛋白质结构和功能位点的分析等功能。该二级数据库的构建为植物激素作用分子机理研究提供了高针对性的植物激素数据源和生物信息学辅助工具。     

植物激素相关核酸和蛋白质二级数据库的构建与应用

以NCBI维护的一级数据库为数据源建立植物激素相关核酸和蛋白质二级数据库。将该二级数据库设计为基因、蛋白质和文献三部分,编写软件从上述数据源中采集数据,并以XML作为中间格式保存,通过解析提交到二级数据库中并集成部分生物信息学工具软件,初步实现了数据检索、统计分析、基于Web的本地化BLAST同源序列检索、序列的自动拼接以及蛋白质结构和功能位点的分析等功能。该二级数据库的构建为植物激素作用分子机理研究提供了高针对性的植物激素数据源和生物信息学辅助工具。     

GenBank.

The GenBank (Registered Trademark symbol) sequence database incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (Web) or Sequin programs to format and send sequence data. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome and protein structure information. MEDLINE (Registered Trademark symbol) s from published articles describing the sequences are included as an additional source of biological annotation through the PubMed search system. Sequence similarity searching is offered through the BLAST series of database search programs. In addition to FTP, Email, and server/client versions of Entrez and BLAST, NCBI offers a wide range of World Wide Web retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the URL: http://www.ncbi.nlm.nih.gov     

Plant genome resources at the national center for biotechnology information

The National Center for Biotechnology Information (NCBI) integrates data from more than 20 biological databases through a flexible search and retrieval system called Entrez. A core Entrez database, Entrez Nucleotide, includes GenBank and is tightly linked to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMed. A suite of more specialized databases for genomes, genes, gene families, gene expression, gene variation, and protein domains dovetails with the core databases to make Entrez a powerful system for genomic research. Linked to the full range of Entrez databases is the NCBI Map Viewer, which displays aligned genetic, physical, and sequence maps for eukaryotic genomes including those of many plants. A specialized plant query page allow maps from all plant genomes covered by the Map Viewer to be searched in tandem to produce a display of aligned maps from several species. PlantBLAST searches against the sequences shown in the Map Viewer allow BLAST alignments to be viewed within a genomic context. In addition, precomputed sequence similarities, such as those for proteins offered by BLAST Link, enable fluid navigation from unannotated to annotated sequences, quickening the pace of discovery. NCBI Web pages for plants, such as Plant Genome Central, complete the system by providing centralized access to NCBI's genomic resources as well as links to organism-specific Web pages beyond NCBI.     

GenBank

The GenBank((R))sequence database incorporates publicly available DNA sequences of >55 000 different organisms, primarily through direct submission of sequence data from individual laboratories and large-scale sequencing projects. Most submissions are made using the BankIt (Web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping and protein structure information, plus the biomedical literature via PubMed. Sequence similarity searching is provided by the BLAST family of programs. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. NCBI also offers a wide range of WWW retrieval and analysis services based on GenBank data. The GenBank database and related resources are freely accessible via the NCBI home page at http://www.ncbi.nlm.nih.gov