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…     

基因表达谱微阵列网络数据库在肿瘤研究中的应用

基因表达谱微阵列数据库是一类可提供存储、查询、下载分析的在线网络数据库,在肿瘤相关领域的研究中提供了大量的数据来源。由于微阵列分析对于无生物/医学信息学专业背景的研究人员仍然有较多困难,致使该数据库的使用尚未普及。本文从数据查询、下载分析和使用方法等方面对常用基因表达谱微阵列数据库进行概述,并对现阶段基因表达微阵列数据库的应用策略进行总结,旨在帮助该领域研究的初学工作者了解数据库的基本知识并推动其在科研工作中的应用。     

NCBI的数据库资源及其应用

NCBI是美国的一个大型生物信息学系统,它主要通过NCBI网站为全世界的科学家服务,它拥有GenBank,RefSeq,UniGene,dbSNP等等多种大型生物学数据库,并且提供了多种数据库查询工具,如：Entrez,PubMed,LocusLink,TaxonomyBrowser等等,以及多种数据库分析资源,对于我们查询文献,人类基因组信息、基因表达、蛋白质结构、肿瘤遗传信息,以及不同种属遗传信息等等有非常大的帮助。是一个非常重要的生物医学资源。     

活植物信息数据库中的植物编码系统

本文概述了南京中山植物园活植物信息数据库中的植物编码系统,重点介绍了植物编码的生成方法。该系统通过将关系数据库ORACLE与Microsoft C所提供的完备的计算模型与关系查询语言的强功能管理手段结合起来,弥补了现行商用数据库的不足,获得了较高的时空效率。     

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…     

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.     

上海昆虫多样性信息系统的设计与建立

利用Access＋ASP＋IIs技术,建立了集害虫信息管理与昆虫编目数据库为一体的上海昆虫多样性管理信息系统。用户可以通过浏览器访问http：／／www．insects．cn进行检索和查询。本文详细阐述了该系统的构建方法,并就目前昆虫多样性信息管理系统建设中存在的问题作了评述。     

古生物信息查询系统

介绍了古生物微机信息查询系统的结构设置（包括数据库设置和功能模块设置），和程序设计（包括数据库结构设计、结构化程序设计、子程序设计、菜单技术程序设计和宏替换函数＆程序设计）。     

生命科学数据库BIOSIS Previews信息资源的查询

生命科学数据库BIOSIS Previews是科技人员有效地利用Internet网络查找国外生命科学信息的世界著名数据库。本文对如何利用BIOSIS Previews查询生命科学相关学术文献作了介绍。     

中国生态农业模式管理信息及决策支持系统的建立

根据全国生态农业试点县建设和典型生态农业模式研究的经验,利用Access数据库技术建立了全国首批生态农业县有关自然资源背景、农业生产水平、生态环境与工程技术等各种基础信息数据库和所推广应用的生态农业模式信息数据库,可快速方便地提供各生态农业县相关信息或知识的查询或编辑．在此基础上,采用了面向对象的推理方法建立了生态农业模式区域决策的知识库体系模型,并利用Visual C^++语言初步开发出生态农业模式的区域决策支持系统,基本上实现了区域生态农业模式的决策推荐．     

Statistics of protein library construction

SUMMARY: We have investigated the statistics associated with constructing and sampling large protein-encoding libraries. Using fairly simple statistics we have written algorithms for estimating the diversity in libraries generated by the most commonly used protocols, including error-prone PCR, DNA shuffling, StEP PCR, oligonucleotide-directed randomization, MAX randomization, synthetic shuffling, DHR, ADO and SISDC. AVAILABILITY: Web interface and C++ source code available at http://guinevere.otago.ac.nz/stats.html. SUPPLEMENTARY INFORMATION: Complete mathematical notes, model assumptions and justification, users' guide and worked examples at above website.     

BLAST++: BLASTing queries in batches

BLAST++ is a tool that is integrated with NCBI BLAST, allowing multiple, say K, queries to be searched against a database concurrently. The results obtained by BLAST++ are identical to that obtained by executing BLAST on each of the K queries, but BLAST++ completes the processing in a much shorter time. AVAILABILITY: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++ Supplementary information: http://xena1.ddns.comp.nus.edu.sg/~genesis/blast++     

Development of SNP markers for C57BL/6N-derived mouse inbred strains

C57BL/6N inbred mice are used as the genetic background for producing knockout mice in large-scale projects worldwide; however, the genetic divergence among C57BL/6N-derived substrains has not been verified. Here, we identified novel single nucleotide polymorphisms (SNPs) specific to the C57BL/6NJ strain and selected useful SNPs for the genetic monitoring of C57BL/6N-derived substrains. Informative SNPs were selected from the public SNP database at the Wellcome Trust Sanger Institute by comparing sequence data from C57BL/6NJ and C57BL/6J mice. A total of 1,361 candidate SNPs from the SNP database could distinguish the C57BL/6NJ strain from 12 other inbred strains. We confirmed 277 C57BL/6NJ-specific SNPs including 10 nonsynonymous SNPs by direct sequencing, and selected 100 useful SNPs that cover all of the chromosomes except Y. Genotyping of 11 C57BL/6N-derived substrains at these 100 SNP loci demonstrated genetic differences among the substrains. This information will be useful for accurate genetic monitoring of mouse strains with a C57BL/6N-derived background.     

COBALT: constraint-based alignment tool for multiple protein sequences

MOTIVATION: A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools. RESULTS: We describe COBALT, a constraint based alignment tool that implements a general framework for multiple alignment of protein sequences. COBALT finds a collection of pairwise constraints derived from database searches, sequence similarity and user input, combines these pairwise constraints, and then incorporates them into a progressive multiple alignment. We show that using constraints derived from the conserved domain database (CDD) and PROSITE protein-motif database improves COBALT's alignment quality. We also show that COBALT has reasonable runtime performance and alignment accuracy comparable to or exceeding that of other tools for a broad range of problems. AVAILABILITY: COBALT is included in the NCBI C++ toolkit. A Linux executable for COBALT, and CDD and PROSITE data used is available at: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt     

Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations

MOTIVATION: Methods involving fuzzy theory have been rarely applied to genetics. We present an open platform for experimentation with fuzzy numbers as a tool to represent imprecise phenotypes in genetic modeling. RESULTS: A C++ library for simulation of genetic information transmission is introduced. The study of genetic linkage was its first goal, though a design so general as possible has been meant. Fuzzy-valued phenotypes are handled by means of fuzzy numbers. AVAILABILITY: ftp://carleos.etsiig.uniovi.es/pub/falin ftp://fisher.ciencias.uniovi.es/pub/falin ftp://bellman.ciencias.uniovi.es/pub/falin Licensed under the GNU General Public License version 2 (see http://www.gnu.org/licenses/gpl.html).     

Changes of adenosine and its A(1) receptor in hypoxic preconditioning.

Effects of hypoxic preconditioning on adenosine (ADO) and its A(1) receptor were studied in Kunming mice. The ADO content and its metabolites in the brain were measured by a specific enzymatic method; a radioligand binding method was used to study the ADO A(1) receptor. The ADO content of the hippocampus in group C (exposure to 4 runs of hypoxia) was markedly higher than that in group A (control, without exposure to hypoxia and B (exposure to 1 run of hypoxia), showing that the ADO content could be cumulatively increased in the hippocampus, which was more sensitive to ischemia and hypoxia, during acute and repeated exposure to hypoxia. A(1) receptor density in group C was significantly lower than in group A and no difference was seen between groups B and C; A(1) receptor affinity in the hippocampus, pons and medula oblongata in group C was significantly higher than in group A, implying that during hypoxic preconditioning there might be some mechanisms preventing A(1) receptor density from decreasing further and making A(1) receptor affinity increase in some brain regions. These results indicate that cumulatively increased ADO in the hippocampus via A(1) receptor may play a neuroprotective role in the CNS as an inhibitory neuromodulator and thus contribute to the formation and development of acute hypoxic adaptation or tolerance.     

急性重复缺氧对小鼠脑组织腺苷及其A1受体的影响

分别应用酶鉴别分光光度法和放射性配体结合法测定小鼠脑组织腺苷（ａｄｅｎｏｓｉｎｅ,ＡＤＯ）含量及Ａ１受体在急性重复缺氧过程中的变化。发现经急性重复缺氧处理的动物全脑内ＡＤＯ含量有一定程度的累积增加,尤其在海马、脑桥和延髓处的增加较为显著;各脑区Ａ１受体的数目显著低于正常对照组,但海马、脑桥和延髓处Ａ１受体的亲和力显著高于正常对照组。结果提示,重复缺氧后虽然脑内Ａ１受体数目减少,但由于海马、脑桥和延髓处Ａ１受体的亲和力升高,累积增加的ＡＤＯ和Ａ１受体结合后,抑制神经细胞兴奋性的作用仍可能得到加强,从而使ＡＤＯ仍能更好地发挥抑制性神经调制作用。     

The influence of evolutionary distance between cross-species microsatellites and primer base-pair composition on allelic dropout rates

Allelic dropouts (ADO) are an important source of genotyping error and because of their negative impact on non-invasive sampling techniques, have become the focus of considerable attention. Previous studies have noted that ADO rates are greater with increasing allele size and in tetranucleotides. It has also been suggested, but not tested, that ADO rates may be higher in studies using cross-species microsatellites and that mutations may play a role in ADO rates. Here we examine the relationship between ADO rates and the relationship between evolutionary distance since divergence time between species for which the microsatellite was designed for and species on which it was used (divergence times), and how this may interact with median allele size. In addition, as the adenosine (A) and thymine (T) content of the primer may increase mutation rates, we also included total % AT content of the primer in the analyses. Finally, we examined whether other commonly associated causes of ADO (i.e. repeat motif length, median allele size and allele number) co-varied. We found that ADO rates were positively associated to divergence time and median allele size. Repeat motif length, median allele size and allele number positively covaried suggesting a link between mutability and these parameters. Results from previous studies that did not correct for co-variation among these parameters may have been confounded. AT content of the primer was positively associated with ADO rates. The best linear regression model contained divergence time, median allele size and total % AT content, explaining 21% of the variation in ADO rates. The available evidence suggests that mutations partly cause ADO and that studies using cross-species microsatellites may be at higher risk of ADO. Based on our results we highlight some important considerations in the selection of microsatellites for all conservation genetic studies.