数据挖掘在生物信息学中的应用——文献计量学视角

基因组和蛋白质结构与功能方面已积累了海量数据。如何从海量数据中获取有效信息成为生物信息学迫切要解决的问题。本文以相关主题词检索文献,分析了该领域历年文章数量、发文最多的机构和作者、被引用频次居前论文、期刊载文量,并对关键词和被引用频次居前论文的作者进行共现分析。我们发现,生物信息学中运用数据挖掘方法的文献逐年增多,该领域30.1%的文献发表在十个期刊上,分类、聚类、特征选择和支持向量机等数据挖掘方法使用较多。本研究描绘了生物信息学与数据挖掘这一交叉领域的研究概况,为后续数据挖掘方法与生物信息学研究相结合提供帮助。     

《生物工程学报》创刊以来全部论文数据库上网

为提高期刊的显示度,加强对历史文档的整理、保护和利用,更好地为科研人员提供信息服务,《生物工程学报》对1985年创刊以来的全部论文进行了数字化制作,建成了回溯文档全文数据库。检索或浏览     

BLASTALIGN在同源基因片段检索中的应用

多序列比对程序的开发在生物信息学中是一个很活跃的研究领域.作为一种新诞生的多序列比对程序,BlastAlign利用blastn算法进行序列比对,并且采用空位替代比对结果中的高变区.目前,该程序主要用于多条基因序列的比对研究.本文则以获取膜翅目小蜂总科28S rDNA D2区基因片段为例,通过应用BlastAlign的序列比对过程,提供一种较为简便和有效的方法,实现从GenBank数据库中检索并筛选特定的同源基因序列,从而克服目前利用关键词或检索式进行检索所存在的局限性.     

《生物工程学报》创刊以来全部论文数据库上网

为提高期刊的显示度,加强对历史文档的整理、保护和利用,更好地为科研人员提供信息服务,《生物工程学报》对1985年创刊以来的全部论文进行了数字化制作,建成了回溯文档全文数据库。检索或浏览我刊已发表的论文请从我刊首页(http://journals.im.ac.cn/cjbcn)"过刊检索"进入,可以按照题目、关键词、年卷期、作者、单位等信息检索,欢迎浏览下载。     

其他

《生物工程学报》创刊以来全部论文数据库上网为提高期刊的显示度,加强对历史文档的整理、保护和利用,更好地为科研人员提供信息服务,《生物工程学报》对1985年创刊以来的全部论文进行了数字化制作,建成了回溯文档全文数据库。检索或浏览我刊已发表的论文请从我刊首页(http://journals.im.ac.cn/cjbcn)"过刊检索"进入,可以按照题目、关键词、年卷期、作者、单位等信息检索,欢迎浏览下载。     

生物信息学软件研究的可视化分析

以Web of Science数据库为数据来源,利用Cite Space和UCINET软件对发表在Nucleic Acids Research期刊上有关生物信息学软件研究的文献做了可视化分析,揭示了该领域的研究力量、作者团队与高被引作者、知识基础、期刊分布、研究热点与前沿,为生物信息学软件的研究和发展提供必要的参考依据。     

生物信息学数据库研究文献引文与热点分析

以Web of Science为数据源,简要概括生物信息学数据库研究的发展趋势。利用Cite Space可视化工具展现生物信息学数据库研究的知识基础和研究热点图谱,为开展生物信息学数据库领域相关的理论研究和实践活动提供借鉴,以便推动生物信息学数据库研究的发展。研究表明：1990年Altschul SF发表的＂局部比对搜索工具——BLAST＂是生物信息学数据库研究的重要知识来源文献;热点主题集中在序列库、基因组数据库、分类数据库、蛋白质数据库、数据库更新、集成系统等。     

甘蔗MYB2转录因子的电子克隆和生物信息学分析

用电子克隆方法获得甘蔗MYB2基因,采用生物信息学方法,对该基因编码蛋白从氨基酸组成、理化性质、跨膜结构域、疏水性/亲水性、亚细胞定位、高级结构及功能域等方面进行了预测和分析。结果表明:甘蔗MYB2基因全长991bp,包含570bp的ORF,编码189个氨基酸。甘蔗MYB2基因包含有MYB功能域,在序列组成、高级结构及活性位点等方面,与玉米等其它植物的MYB2基因具有高度的相似性。研究结果为该基因的实验克隆奠定基础。     

基于共词分析的国内生物信息学热点领域研究

利用共词分析和可视化方法对生物信息学的关键词进行聚类分析,探讨该研究领域的学科分类和热点内容.以中国知网、中华医学会数据库中期刊论文为统计来源,对1998～2013年间的5 707篇生物信息学相关文献进行计量分析,提取出40个高频关键词.利用ROST软件得到关键词共词矩阵,在此基础上利用SPSS进行因子分析、聚类分析和多维尺度分析.结合因子分析和聚类分析将生物信息学领域主要研究内容分为7类,结合多维尺度分析对研究热点及变化趋势进行了初步探讨.研究结果较为客观地反映了当前生物信息学领域的学科分类和研究热点,为科研人员进行生物信息学研究提供一些思路.     

国际生物信息学研究的可视化分析

利用当前主流的信息可视化分析软件Cite Space对2005~2014年间SCI收录的生物信息学的5种高影响力外文期刊所刊载论文的题录数据进行统计和可视化分析,绘制该领域的关键词共现、膨胀词共现、经典文献共现、高被引文献共现和关键节点文献共现的网络可视化图谱,试图揭示生物信息学领域的研究热点、研究前沿以及知识基础,以期帮助研究人员了解该领域在国际范围内的研究态势。     

Optimizing search conditions for the mass fingerprint-based identification of proteins

The two central problems in protein identification by searching a protein sequence collection with MS data are the optimal use of experimental information to allow for identification of low abundance proteins and the accurate assignment of the probability that a result is false. For comprehensive MS-based protein identification, it is necessary to choose an appropriate algorithm and optimal search conditions. We report a systematic study of the quality of PMF-based protein identifications under different sequence collection search conditions using the Probability algorithm, which assigns the statistical significance to each result. We employed 2244 PMFs from 2-DE-separated human blood plasma proteins, and performed identification under various search constraints: mass accuracy (0.01-0.3 Da), maximum number of missed cleavage sites (0-2), and size of the sequence collection searched (5.6 x 10(4)-1.8 x 10(5)). By counting the number of significant results (significance levels 0.05, 0.01, and 0.001) for each condition, we demonstrate the search condition impact on the successful outcome of proteome analysis experiments. A mass correction procedure utilizing mass deviations of albumin matching peptides was tested in an attempt to improve the statistical significance of identifications and iterative searching was employed for identification of multiple proteins from each PMF.     

THE COLLECTION OF FOUND IVORY IN MURCHISON FALLS NATIONAL PARK, UGANDA

The paper concerns the circumstances surrounding the collection of ivory from dead elephants, with particular reference to Murchison Falls National Park. The characteristics of the interval between death and complete disintegration of an elephant are described. These, combined with observations of known age skeletons, comprised the criteria used in classifying skeletons found from the air into three relative age classes. Average annual mortality is estimated for the population north of the Nile (MFPN) at 147 animals yielding 1945 kg of ivory, and for that south of the Nile (MFPS) at 474 animals yielding 7497 kg ivory. Park-found ivory records are analyzed for the 11 y 1959–69. The expected age distribution of deaths is compared with the observed. For MFPN a bias in favour of large (male) tusks is present, explicable by the concentration of ranger search effort in areas of known high male density. For MFPS a bias towards small tusks is thought to be caused by elephants wounded outside the park dying inside it. The National Park recovers an average of 27.6 % of its available ivory per annum, with large annual fluctuations probably correlated with the incidence of wounding outside the park. High losses to poachers are evident. An aerial search for ivory showed a tendency for elephants to die near watercourses. A finding rate of one carcass every 4.3 km of watercourse was obtained. As only 5 % of carcasses still had tusks the aerial searching was prematurely terminated. The results indicated a finding efficiency of 26.4% of the available current year carcasses. Comparative costing suggests that ground searching would be a more efficient method of finding ivory than aerial searching. The high value of the available ivory in Murchison and other areas justifies intensive searching. The low collection rates prevailing in East Africa are largely attributable to the absence of appropriate search efforts.     

Search strategies of tyrant flycatchers

Aspects of searching behaviour among free-living South American flycatchers (Aves: Tyrannidae) are compared quantitatively. Flycatchers forage with stationary searching periods, followed either by an attempted prey capture (sally) or a ‘give-up’ flight to a new perch. Search times are proportional to body size within each of three categories of foraging behaviour: aerial hawking, sally-gleaning, and perch-gleaning. Over the family as a whole, search times are directly proportional to the size of the visual field scanned during the search. Intraspecific variations in search times are caused by local variations in prey density or visual complexity of the habitat. Between foraging modes, differences in searching and movement patterns are related to prey dispersion characteristics. Aerial hawkers regularly return to favoured perches, but foliage gleaners, which reduce the resources surrounding a perch by sallying only once, rarely return to a perch. In contrast to aerial hawkers, foliage gleaners appear to follow an organized scanning procedure on each perch, by searching nearby surfaces before they examine more distant prey substrates. Throughout the family, the median flight distance after a perch is abandoned is approximately twice the median search radius. Comparisons of search time distributions preceding sallies with those preceding give-up flights suggest that there is no single, optimal give-up time in a given habitat. Foliage-gleaning species appear to assess the amount of search time each perch warrants, presumably based on the degree of complexity of the search area. They either sally at prey before that time, or give-up when the allotted time has elapsed.     

基于谱图库的蛋白质鉴定策略研究进展

基于质谱的蛋白质组学快速发展,蛋白质质谱数据也呈指数式增长。寻找速度快、准确度高以及重复性好的鉴定方法是该领域的一项重要任务。谱图库搜索策略直接比较实验谱图与谱图库中的真实谱图,充分利用了谱图中的丰度、非常规碎裂模式和其他的一些特征,使得搜索更加快速和准确,成为蛋白质组学的主流鉴定方法之一。文中介绍基于谱图库的蛋白质组质谱数据鉴定策略,并针对其中两个关键步骤——谱图库构建方法和谱图库搜索方法进行深入介绍,探讨了谱图库策略的进展和挑战。     

Proteogenomics to discover the full coding content of genomes: A computational perspective

Proteogenomics has emerged as a field at the junction of genomics and proteomics. It is a loose collection of technologies that allow the search of tandem mass spectra against genomic databases to identify and characterize protein-coding genes. Proteogenomic peptides provide invaluable information for gene annotation, which is difficult or impossible to ascertain using standard annotation methods. Examples include confirmation of translation, reading-frame determination, identification of gene and exon boundaries, evidence for post-translational processing, identification of splice-forms including alternative splicing, and also, prediction of completely novel genes. For proteogenomics to deliver on its promise, however, it must overcome a number of technological hurdles, including speed and accuracy of peptide identification, construction and search of specialized databases, correction of sampling bias, and others. This article reviews the state of the art of the field, focusing on the current successes, and the role of computation in overcoming these challenges. We describe how technological and algorithmic advances have already enabled large-scale proteogenomic studies in many model organisms, including arabidopsis, yeast, fly, and human. We also provide a preview of the field going forward, describing early efforts in tackling the problems of complex gene structures, searching against genomes of related species, and immunoglobulin gene reconstruction.     

Risky mate search and mate preference in the golden orb-web spider (Nephila plumipes)

Mate searching is a risky behavior that decreases survival byincreasing predation risk and the risk of energy depletion.However, few studies have quantified actual mortality duringmate search, making it difficult to predict mate searching andmating strategies. Using a mark and recapture study, we examinedmate-searching success in a highly sexually dimorphic species,the golden orb-web spider (Nephila plumipes). We show that despitethe high-density aggregations of this species, male survivalduring mate searching is extremely low (36%) and is phenotypeindependent. Surprisingly, males that survived mate search werein better condition after recapture than prior to release, mostlikely due to kleptoparasitism on females' webs. In a complementaryrelease experiment in a field enclosure, we show that malesare choosy and adjust their choice of female depending on theirown condition and weight. Thus, the high mortality rate of searchingmales in the field may be a cost of choosiness because releasedmales traveled further than necessary to settle on females.Although males were choosy about female phenotypes, they didnot avoid webs with rival males already present. This suggeststhat the cost of continued searching outweighs the cost of competitionbut not the cost of mating with certain females. Further examinationsof mate-searching risk in other species in reference to theirmating system and environmental conditions are necessary todetermine the occurrence and effects of high mortality ratesduring searching.     

A step-by-step guide to systematically identify all relevant animal studies

Before starting a new animal experiment, thorough analysis of previously performed experiments is essential from a scientific as well as from an ethical point of view. The method that is most suitable to carry out such a thorough analysis of the literature is a systematic review (SR). An essential first step in an SR is to search and find all potentially relevant studies. It is important to include all available evidence in an SR to minimize bias and reduce hampered interpretation of experimental outcomes. Despite the recent development of search filters to find animal studies in PubMed and EMBASE, searching for all available animal studies remains a challenge. Available guidelines from the clinical field cannot be copied directly to the situation within animal research, and although there are plenty of books and courses on searching the literature, there is no compact guide available to search and find relevant animal studies. Therefore, in order to facilitate a structured, thorough and transparent search for animal studies (in both preclinical and fundamental science), an easy-to-use, step-by-step guide was prepared and optimized using feedback from scientists in the field of animal experimentation. The step-by-step guide will assist scientists in performing a comprehensive literature search and, consequently, improve the scientific quality of the resulting review and prevent unnecessary animal use in the future.     

Building and searching tandem mass (MS/MS) spectral libraries for peptide identification in proteomics

Spectral library searching is an emerging approach in peptide identifications from tandem mass spectra, a critical step in proteomic data analysis. In spectral library searching, a spectral library is first meticulously compiled from a large collection of previously observed peptide MS/MS spectra that are conclusively assigned to their corresponding amino acid sequence. An unknown spectrum is then identified by comparing it to all the candidates in the spectral library for the most similar match. This review discusses the basic principles of spectral library building and searching, describes its advantages and limitations, and provides a primer for researchers interested in adopting this new approach in their data analysis. It will also discuss the future outlook on the evolution and utility of spectral libraries in the field of proteomics.     

Announcement—guidance document for acquiring reliable data in ecological restoration projects

The Laurentian Great Lakes are undergoing intensive ecological restoration in Canada and the United States. In the United States, an interagency committee was formed to facilitate implementation of quality practices for federally funded restoration projects in the Great Lakes basin. The Committee's responsibilities include developing a guidance document that will provide a common approach to the application of quality assurance and quality control (QA/QC) practices for restoration projects. The document will serve as a “how‐to” guide for ensuring data quality during each aspect of ecological restoration projects. In addition, the document will provide suggestions on linking QA/QC data with the routine project data and hints on creating detailed supporting documentation. Finally, the document will advocate integrating all components of the project, including QA/QC applications, into an overarching decision‐support framework. The guidance document is expected to be released by the U.S. EPA Great Lakes National Program Office in 2017.     

YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation

A fundamental challenge facing biologists is to identify DNA binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated. The program YMF identifies good candidates for such binding sites by searching for statistically overrepresented motifs. More specifically, YMF enumerates all motifs in the search space and is guaranteed to produce those motifs with greatest z-scores. This note describes the YMF web software, available at http://bio.cs.washington.edu/software.html.