利用SWISS-PROT网上获取生物信息学资源

生物信息学是是采用数学、统计学和计算机方法对生物学数据信息进行采集、存储、传播、分析、归类、解释的科学[1].Internet网络是信息传输、检索、获取、交流的重要手段.当前,在Internet网上可以查询到大量的生物信息学数据库,其中SWISS-PROT蛋白质序列数据库是网上生物信息学最核心的3个数据库之一.通过该数据库,可以较完整地获得生物大分子的序列信息.同时,研究者也可以将测定的序列信息通过该数据库予以认定、发表、交流.本文主要探讨SWISS-PROT蛋白质序列数据库的特点、检索方法及利用Internet获取蛋白质序列信息.     

利用E-mail检索Inter网上的昆虫基因信息

在昆虫分子生物学研究中 ,常常需要了解昆虫的基因序列或对基因序列进行分析比较。随着 Internet的迅速发展 ,互连网上的昆虫学资源也日益丰富。利用 E-mail可以免费、迅速地获得美国国家生物技术信息中心提供的有关核酸和蛋白质序列与结构以及出版物的信息 ,其中也包括昆虫的信息。只需要向地址为query@ncbi.nlm.nih.gov的服务器发送按下文格式书写的 E-mail,若网络通畅 ,几分钟就可以收到对方按查询要求发回的 E-mail。该服务器提供的检索范围几乎囊括了世界上所有著名的相关数据库 ,其中核酸序列数据库包括 :Gen Bank,EMBL,DDBJ,db…     

电子通讯与生物大分子序列分析

随着核酸和蛋白质序列数据的急剧增加和分子生物学家对最新序列数据的需要,用磁带、磁盘甚至光盘已不能满足大量数据的存贮和数据库迅速更新的要求。另一方面长期维持订购一套(或几套)核酸和蛋白质数据库、购买不断涌现的新的序列分析软件也是一项巨大的开支。近年来,随着全球性信息高速公路的建设。越来越多的分子生物学数据库和软件与国际计算机网络系统相连,任何一台与之连网的计算机都可以利用这些软件和信息资源。用户不但能检索到最新的     

用微型机TRS-80(Ⅰ)实现核酸序列资料管理系统

本文报道了能实现对核酸序列资料进行分析处理及其管理的TRS-80(Ⅰ)微型计算机的应用程序。该程序系统是由一组相互独立的、具有多种功能的程序文件通过主程序文件的相互关联而组成,并以文件的形式存贮于软磁盘中。整个管理系统是用磁盘BASICⅡ语言设计编制的。在TRS-80微型机的New DOS操作系统下,通过文件操作和文件存取的方式而实现对核酸序列资料的管理。该管理系统能提供12种功能,并能方便地加以扩充。它基本上能满足用户对于核酸序列一级结构的分析、处理的需要。另外该系统中的大多数程序文件也能用于氨基酸序列的分析处理。     

利用SWISS-PROT网获取生物信息学资源

生物信息学是是采用数学、统计学和计算机方法对生物学数据信息进行采集、存储、传播、分析、归类、解释的科学[1] 。Ｉｎｔｅｒｎｅｔ网络是信息传输、检索、获取、交流的重要手段。当前 ,在Ｉｎｔｅｒｎｅｔ网上可以查询到大量的生物信息学数据库 ,其中ＳＷＩＳＳ ＰＲＯＴ蛋白质序列数据库是网上生物信息学最核心的 3个数据库之一。通过该数据库 ,可以较完整地获得生物大分子的序列信息。同时 ,研究者也可以将测定的序列信息通过该数据库予以认定、发表、交流。本文主要探讨ＳＷＩＳＳ ＰＲＯＴ蛋白质序列数据库的特点、检索方法及利用Ｉ…     

SeqHunter：序列搜索与分析的生物信息学软件包

利用Microsoft Visual Basic 6.0脚本,开发了一个在Windows平台下使用的生物信息学软件包SeqHunter;该软件包以简便的图形界面操作方式,可以实现本地化Blast,序列提取、比对与分析,序列数据库建立和管理等多种常用功能,为基因功能分析与大规模基因组数据挖掘提供了一个实用工具。     

2019新型冠状病毒信息库

2019年12月在中国武汉开始爆发的新型肺炎已造成全球25个国家/地区的31516人感染、638人死亡(截止2020年2月7日16时),引起该肺炎的病毒被世界卫生组织命名为2019新型冠状病毒(2019-nCoV)。为促进2019-nCoV数据共享应用并及时向全球公众提供病毒的相关信息,国家生物信息中心(CNCB)/国家基因组科学数据中心(NGDC)建立了2019新型冠状病毒信息库(2019nCoVR,https://bigd.big.ac.cn/ncov)。该信息库整合了来自德国全球流感病毒数据库、美国国家生物技术信息中心、深圳(国家)基因库、国家微生物科学数据中心及CNCB/NGDC等机构公开发布的2019-nCoV核苷酸和蛋白质序列数据、元信息、学术文献、新闻动态、科普文章等信息,开展了不同冠状病毒株的基因组序列变异分析并提供可视化展示。同时,2019nCoVR无缝对接CNCB/NGDC的相关数据库,提供新测序病毒株系的基因组原始测序数据、组装后序列的在线汇交、管理与共享、国际数据库同步发布等数据服务。本文对2019nCoVR数据汇交、管理、发布及使用等进行全面阐述,以方便用户了解该信息库各项功能及数据状况,为加速开展病毒的分类溯源、变异演化、快速检测、药物研发以及新型肺炎的精准预防与治疗等研究提供重要基础。     

基于Web的水稻芯片数据注释和分析平台

国际水稻基因组测序计划(IEGSP)顺利完成, 水稻基因的研究也进入了后基因组研究阶段. 水稻基因芯片数据注释分析是一项重要的功能基因组学研究内容, 它为理解水稻基因的生物学意义提供了帮助. 本研究开发了一个基于Web的水稻基因芯片数据注释和分析平台(RiceChip), 它比同类的注释数据库更加全面快捷. 本平台共由5个功能模块组成: BioChip模块为水稻基因表达数据提供快速检索和高级检索, 可依次按照Probe Set ID, Locus ID, Analysis Name等字段进行检索; BioAnno模块整合多个生物学数据库, 为水稻基因提供基因功能、蛋白质结构、生物代谢途径以及转录调控等方面的注释信息; BioSeq模块则收集水稻基因组的序列信息, 支持对水稻基因与芯片探针的序列查询; BioView模块是系统图形可视化的核心模块, 提供友好的访问界面与结果输出, 方便研究人员使用; BioAnaly模块结合R/Bioconductor统计分析工具提供高通量芯片数据的在线分析. 本系统从不同的方面依次提供了数据检索、基因注释、序列分析、数据可视化和数据分析等功能, 其数据收集的全面性与功能分析的强大性在同类水稻基因芯片数据注释和分析平台中都较突出.     

基于WebGIS的植物园植物物种管理信息系统

鉴于植物园现代化管理和国内外植物资源信息交流的迫切需要,利用WebGIS系统集成技术在Internet上建立了中国科学院武汉植物园植物物种管理信息系统。系统实现了基于网络的图形属性数据的双向查询,并具有新增、编辑、缩放、漫游、定位等功能,为植物迁地保育的动态管理提供了管理工具,为科研、科普等应用部门和科技人员提供了获取植物物种信息的工作平台。文中详细介绍了该系统的设计要求、数据来源、开发运行环境、数据库构成、系统功能等。     

Bioinformatics: A Practical Guide to the Analysis of Genes & Proteins, (third editon). * Edited by Andreas D. Baxevanis and B.F. Francis Ouellette * New York: John Wiley & Sons; * ISBN: 0471 478784; 540pp.; 2004; $79.95.

In the post-genomics era of contemporary biological research,it is imperative for molecular biologists to survey and utilizebioinformatic algorithms, software tools and databases. Theprosperity of bioinformatic resources in the public domain isevidently an answer to the needs of molecular biologists, whichin return post new challenges and point out to new researchdirections for bioinformaticians,     

Nucleic acid and protein sequence databases

Nucleic acid and protein sequences contain a wealth of informationof interest to molecular biologists. The advent of molecularsequence databases provides a unique opportunity for the computeranalysis of all available sequences. Sequence databases servetwo main functions: (i) to facilitate comparisons with newlydetermined sequences, and (ii) to act as a source of data forthe generation and testing of hypotheses concerning molecularsequence organisation and evolution. The large amounts of sequencedata now becoming available require that algorithms for databasesearching be fast and efficient and considerable progress isbeing made in this area.     

The European Bioinformatics Institute (EBI) databases.

The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities.     

Genomics made easier: An introductory tutorial to genome datamining

Integrated genome databases – such as the UCSC, Ensembl and NCBI MapViewer databases – and their associated data querying and visualization interfaces (e.g. the genome browsers) have transformed the way that molecular biologists, geneticists and bioinformaticists analyze genomic data. Nevertheless, because of the complexity of these tools, many researchers take advantage of only a fraction of their capabilities. In this tutorial, using examples from medical genetics and alternative splicing, I describe some of the biological questions that can be addressed with these techniques. I also show why doing so typically is more effective than using alternative methods and indicate some of the resources available for learning more about the advanced capabilities of these powerful tools.     

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

Background  

Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST) or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary.     

Overview of the LiMB database.

The rapidly increasing number of databases relevant to molecular biology has given rise to a need for a coordinated effort to identify, characterize, and link them. The LiMB database, which contains information about molecular biology and related databases, is a step in that direction. It serves molecular biologists seeking data sets containing information relevant to their research, and is also intended to anticipate the needs of database designers and managers building software links for related data sets. We present an abbreviated version of the database here; the full database is available free of charge as described below.     

Informatics - genome and genetic databases

Databases for biologists are becoming increasingly important. Some of these can be regarded as ‘core’ resources, such as the bibliographic databases, whereas others are of greater interest to specialists. As comparative genomics develops, however, even databases limited in their scope (e.g. to a single organism) are of great interest to a wider community.     

The European Bioinformatics Institute (EBI) databases.

This paper describes the databases and services of the European Bioinformatics Institute (EBI). In collaboration with DDBJ and GenBank/NCBI, the EBI maintains and distributes the EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence Database, in collaboration with Amos Bairoch of the University of Geneva. Over thirty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists, are also available. The EBI network services include database searching, entry retrieval, and sequence similarity searching facilities.     

GenBank.

The GenBank(R) sequence database (http://www.ncbi.nlm.nih.gov/) 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 (WWW) or Sequin programs to send their 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(R) abstracts from published articles describing the sequences are also included as an additional source of biological annotation. Sequence similarity searching is offered through the BLAST series of database search programs. In addition to FTP, e-mail and server/client versions of Entrez and BLAST, NCBI offers a wide range of World Wide Web retrieval and analysis services of interest to biologists.     

Java editor for biological pathways

SUMMARY: A visual Java-based tool for drawing and annotating biological pathways was developed. This tool integrates the possibilities of charting elements with different attributes (size, color, labels), drawing connections between elements in distinct characteristics (color, structure, width, arrows), as well as adding links to molecular biology databases, promoter sequences, information on the function of the genes or gene products, and references. It is easy to use and system independent. The result of the editing process is a PNG (portable network graphics) file for the images and XML (extended markup language) file for the appropriate links.