糖类的生物信息学资源

生物信息学在推动遗传学和蛋白质科学的研究领域中,已发挥了举足轻重的作用.相比较而 言,糖科学产生的信息还比较有限,随着人们对糖类分子的关注,糖生物学的发展也出现新 的契机,其信息正在飞速地增长.对已经获得的糖类相关知识进行系统整合就显得越来越有 必要,许多研究型数据库和免费工具已应运而生,并且数目在不断扩大,正成为科学工作者 非常便利的工具.但到目前为止,许多数据库或者网络预测工具在文献中很少提及或难以找 到,给研究者带来了不少的麻烦.部分原因是数据库资源本身数据不断在更新,人机界面也 变得越方便和人性化,另外就是人们对于这些新型的研究工具了解较少.这篇综述介绍了 目前网络上最常用的糖类生物信息学资源,包括糖的一级结构,分析测试数据、构象,酶, 凝集素,糖蛋白等方面的各种数据库.     

Identifications of pathogens - a bioinformatic point of view

Over the past 15 years, microbiology has undergone a momentous shift toward molecular methods. New sequences appear daily in the public databases and new computer tools and web servers are published on a regular basis. Major advances in molecular identifications of pathogens have been made because new biotechnology methods have appeared that often require a thorough in silico analysis of sequences. However, significant difficulties partly remain in developing efficient methods because the public databases contain many poorly annotated or partial sequences (often of environmental origin) and also because there are few dedicated web servers and curated databases.     

Biotic stress resistance in agriculture through antimicrobial peptides

Antimicrobial peptides (AMPs) are the hosts' defense molecules against microbial pathogens and gaining extensive research attention worldwide. These have been reported to play vital role of host innate immunity in response to microbial challenges. AMPs can be used as a natural antibiotic as an alternative of their chemical counterpart for protection of plants/animals against diseases. There are a number of sources of AMPs including prokaryotic and eukaryotic organisms and are present, both in vertebrates and invertebrates. AMPs can be classified as cationic or anionic, based on net charges. Large number of databases and tools are available in the public domain which can be used for development of new genetically modified disease resistant varieties/breeds for agricultural production. The results of the biotechnological research as well as genetic engineering related to AMPs have shown high potential for reduction of economic losses of agricultural produce due to pathogens. In this article, an attempt has been made to introduce the role of AMPs in relation to plants and animals. Their functional and structural characteristics have been described in terms of its role in agriculture. Different sources of AMPs and importance of these sources has been reviewed in terms of its availability. This article also reviews the bioinformatics resources including different database tools and algorithms available in public domain. References of promising biotechnology research in relation to AMPs, prospects of AMPs for further development of genetically modified varieties/breeds are highlighted. AMPs are valuable resource for students, researchers, educators and medical and industrial personnel.     

BioWareDB: the biomedical software and database search engine

A wealth of bioinformatics tools and databases has been created over the last decade and most are freely available to the general public. However, these valuable resources live a shadow existence compared to experimental results and methods that are widely published in journals and relatively easily found through publication databases such as PubMed. For the general scientist as well as bioinformaticists, these tools can deliver great value to the design and analysis of biological and medical experiments, but there is no inventory presenting an up-to-date and easily searchable index of all these resources. To remedy this, the BioWareDB search engine has been created. BioWareDB is an extensive and current catalog of software and databases of relevance to researchers in the fields of biology and medicine, and presently consists of 2800 validated entries. AVAILABILITY: BioWareDB is freely available over the Internet at http://www.biowaredb.org/     

Website review: how to get the best from fission yeast genome data

Researchers are increasingly depending on various centralized resources to access the vast amount of information reported in the literature and generated by systematic sequencing and functional genomics projects. Biological databases have become everyday working tools for many researchers. This dependency goes both ways in that the databases require continuous feedback from the research community to maintain accurate, reliable, and upto- date information. The fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genome era of this popular model organism. Here, we provide an overview of relevant databases available, or being developed, together with a compilation of Internet resources containing useful information and tools for fission yeast.     

Plant genome databases: from references to inference tools

Plant genome databases play an important role in the archiving and dissemination of data arising from the international genome projects. Recent developments in bioinformatics, such as new software tools, programming languages and standards, have produced better access across the Internet to the data held within them.An increasing emphasis is placed on data analysis and indeed many resources now provide tools allied to the databases, to aid in the analysis and interpretation of the data. However, a considerable wealth of information lies untapped by considering the databases as single entities and will only be exploited by linking them with a wide range of data sources. Data from research programs such as comparative mapping and germplasm studies may be used as tools, to gain additional knowledge but without additional experimentation. To date, the current plant genome databases are not yet linked comprehensively with each other or with these additional resources, although they are clearly moving toward this. Here, the current wealth of public plant genome databases is reviewed, together with an overview of initiatives underway to bind them to form a single plant genome infrastructure.     

RNAcentral: A vision for an international database of RNA sequences

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.     

Farm animal genome databases

The requirements for bioinformatics resources to support genome research in farm animals is reviewed.The resources developed to meet these needs are described. Resource databases and associated tools have been developed to handle experimental data. Several of these systems serve the needs of multinational collaborations. Genome databases have been established to provide contemporary summaries of the status of genome maps in a range of farm and domestic animals along with experimental details and citations. New resources and tools will be required to address the informatics needs of emerging technologies such as microarrays. However, continued investment is also required to maintain the currency and utility of the current systems, especially the genome databases.     

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition

The ever-increasing generation of, and corresponding interest in, molecular interaction data has lead to the establishment of a number of high-quality molecular interaction databases which manually curate interaction data extracted from the literature. In order to effectively share the curation load, and ensure that data is stored in and accessible from multiple sources, these databases have united to form the IMEx consortium. All of the IMEx databases also accept direct deposition of interaction data from authors prior to publication, thus both assisting the scientist in preparing the dataset for publication and ensuring that its subsequent representation in the public domain databases is fully accurate. This article walks the potential submitter through the various routes by which data may be deposited with the databases and describes the tools which have been developed to assist in this process.     

利用TIGR番茄基因索引分析挖掘果实成熟相关基因

目前,互联网上提供许多关于基因及其相关信息的数据库,从这些资料库中提取的资料信息,可用于遗传,生化,分子生物学等各种形式的研究。TIGR Tomato Gene Index数据库中的信息为研究番茄果实成熟开辟了新思路。本研究通过对该数据库的分析,发现了一些在番茄果实成熟过程中差异表达的基因。并进一步通过基因芯片软件和文献挖掘的方法对这些基因进行了分析,结果发现了一些新的与果实成熟相关的基因。这对研究番茄果实成熟提供有价值的信息和思路。     

Immunoinformatics comes of age

With the burgeoning immunological data in the scientific literature, scientists must increasingly rely on Internet resources to inform and enhance their work. Here we provide a brief overview of the adaptive immune response and summaries of immunoinformatics resources, emphasizing those with Web interfaces. These resources include searchable databases of epitopes and immune-related molecules, and analysis tools for T cell and B cell epitope prediction, vaccine design, and protein structure comparisons. There is an agreeable synergy between the growing collections in immune-related databases and the growing sophistication of analysis software; the databases provide the foundation for developing predictive computational tools, which in turn enable more rapid identification of immune responses to populate the databases. Collectively, these resources contribute to improved understanding of immune responses and escape, and evolution of pathogens under immune pressure. The public health implications are vast, including designing vaccines, understanding autoimmune diseases, and defining the correlates of immune protection.     

Public proteomic MS repositories and pipelines: available tools and biological applications

As proteomic MS has increased in throughput, so has the demand to catalogue the increasing number of peptides and proteins observed by the community using this technique. As in other 'omics' fields, this brings obvious scientific benefits such as sharing of results and prevention of unnecessary repetition, but also provides technical insights, such as the ability to compare proteome coverage between different laboratories, or between different proteomic platforms. Journals are also moving towards mandating that proteomics data be submitted to public repositories upon publication. In response to these demands, several web-based repositories have been established to store protein and peptide identifications derived from MS data, and a similar number of peptide identification software pipelines have emerged to deliver identifications to these repositories. This paper reviews the latest developments in public domain peptide and protein identification databases and describes the analysis pipelines that feed them. Recent applications of the tools to pertinent biological problems are examined, and through comparing and contrasting the capabilities of each system, the issues facing research users of web-based repositories are explored. Future developments and mechanisms to enhance system functionality and user-interfacing opportunities are also suggested.     

全基因组测序在病原菌分型与溯源中的应用研究进展

细菌分子分型已成为监测细菌感染性疾病的暴发流行与明确病原菌传播途径的重要工具。随着全基因组测序技术的日益兴起,公共数据库中已产生大量的细菌基因组数据,迫切需要研究人员充分认识和理解该技术,并掌握多种生物信息学工具挖掘并解读测序数据。本文系统概述了全基因组测序技术与生物信息学工具在病原菌分型与溯源中的应用,并对全基因组测序技术在临床诊疗实践中存在的挑战以及未来应用前景进行了探讨。     

Association between fatty acid compositions and genotypes of FABP4 and LXR-alpha in Japanese Black cattle

Background

Single nucleotide polymorphisms (SNPs) and small insertions or deletions (indels) are the most common type of polymorphisms and are frequently used for molecular marker development. Such markers have become very popular for all kinds of genetic analysis, including haplotype reconstruction. Haplotypes can be reconstructed for whole chromosomes but also for specific genes, based on the SNPs present. Haplotypes in the latter context represent the different alleles of a gene. The computational approach to SNP mining is becoming increasingly popular because of the continuously increasing number of sequences deposited in databases, which allows a more accurate identification of SNPs. Several software packages have been developed for SNP mining from databases. From these, QualitySNP is the only tool that combines SNP detection with the reconstruction of alleles, which results in a lower number of false positive SNPs and also works much faster than other programs. We have build a web-based SNP discovery and allele detection tool (HaploSNPer) based on QualitySNP.

Results

HaploSNPer is a flexible web-based tool for detecting SNPs and alleles in user-specified input sequences from both diploid and polyploid species. It includes BLAST for finding homologous sequences in public EST databases, CAP3 or PHRAP for aligning them, and QualitySNP for discovering reliable allelic sequences and SNPs. All possible and reliable alleles are detected by a mathematical algorithm using potential SNP information. Reliable SNPs are then identified based on the reconstructed alleles and on sequence redundancy.

Conclusion

Thorough testing of HaploSNPer (and the underlying QualitySNP algorithm) has shown that EST information alone is sufficient for the identification of alleles and that reliable SNPs can be found efficiently. Furthermore, HaploSNPer supplies a user friendly interface for visualization of SNP and alleles. HaploSNPer is available from http://www.bioinformatics.nl/tools/haplosnper/.     

The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy server

Since it was launched in 1993, the ExPASy server has been and is still a reference in the proteomics world. ExPASy users access various databases, many dedicated tools, and lists of resources, among other services. A significant part of resources available is devoted to two-dimensional electrophoresis data. Our latest contribution to the expansion of the pool of on-line proteomics data is the World-2DPAGE Constellation, accessible at http://world-2dpage.expasy.org/. It is composed of the established WORLD-2DPAGE List of 2-D PAGE database servers, the World-2DPAGE Portal that queries simultaneously world-wide proteomics databases, and the recently created World-2DPAGE Repository. The latter component is a public standards-compliant repository for gel-based proteomics data linked to protein identifications published in the literature. It has been set up using the Make2D-DB package, a software tool that helps building SWISS-2DPAGE-like databases on one's own Web site. The lack of necessary informatics infrastructure to build and run a dedicated website is no longer an obstacle to make proteomics data publicly accessible on the Internet.     

Virus variation resources at the National Center for Biotechnology Information: dengue virus

Background  

There is an increasing number of complete and incomplete virus genome sequences available in public databases. This large body of sequence data harbors information about epidemiology, phylogeny, and virulence. Several specialized databases, such as the NCBI Influenza Virus Resource or the Los Alamos HIV database, offer sophisticated query interfaces along with integrated exploratory data analysis tools for individual virus species to facilitate extracting this information. Thus far, there has not been a comprehensive database for dengue virus, a significant public health threat.     

Analysis of the Candida albicans proteome. II. Protein information technology on the Net (update 2002)

Candida albicans is an important fungal model organism of noteworthy clinical interest in modern medicine. Different initiatives addressing its sequencing and physical mapping have been carried out. The C. albicans genome sequence is currently near to completion at Stanford University, heralding new challenges in proteomic research and functional analyses of its gene products. This review presents an update of the most relevant data resources that are available through the World Wide Web to scientists working in the area of the analysis of the C. albicans proteome. An overview of the current status of the main universal protein sequence databases and specialized data collections for C. albicans is given. Various issues of the single public C. albicans 2D-PAGE database are also described, highlighting the significance of setting up graphical query interface-based databanks to visualize 2D-PAGE images through the Net. Finally, we also emphasize the pressing need to create a "cyber-bioknowledge library" that will integrate all the databases developed at the different levels for the understanding of life processes as well as bioinformatic tools for interpreting this deluge of data generated through the Internet.     

Relax with CouchDB--into the non-relational DBMS era of bioinformatics

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services.