The Jalview Resource for Sequence Analysis and Annotation

用于序列分析和注释的 Jalview 资源

• 批准号: BB/L020742/1
• 负责人: Geoffrey Barton
• 金额: $ 65.45万
• 依托单位: University of Dundee
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL020742%2F1
• 关键词: Jalview; Resource; Sequence; Analysis; Annotation

Comparison is a central part of everyone's daily life. If two objects look similar, then a first guess is that they might have similar functions. Comparison of the biological molecules DNA, RNA and proteins from different individuals or species is central to understanding what each molecule does. DNA, RNA and protein molecules can be represented as long "words" of a few letters up to thousands or even millions of letters in length. It is these words, or "sequences" that are compared by computer programs. For example, comparison of a protein sequence from a plant disease-causing bacterium with that from the plant may suggest ways to design a treatment to kill the bacterium and not the plant. Ideally, more than two sequences are compared at the same time as this makes it easier to spot common features. This process is called "multiple sequence alignment" and is one of the most powerful techniques available in modern biology. Easy-to-use but feature-rich interactive computer programs are essential to visualise and enable the most information to be extracted from multiple sequence alignments. Jalview, is the most widely used program for visualising sequence alignments and editing them. It is installed on over 55,000 computers world-wide, on hundreds of thousands of web pages, and is in daily use by thousands of scientists and students. Jalview not only allows alignments to be viewed coloured and edited, but also exploits the internet to connect to over 1,400 sources of sequences and annotations on those sequences. In addition, Jalview exploits state-of-the-art internet technology to connect to computer servers that can perform large calculations on the sequences and return these to the user in a few seconds or minutes. In this way the program puts a mass of human knowledge at the fingertips of the scientist and so saves them a huge amount of time in exploring the function of their favourite protein, DNA or RNA molecule. Some databases of alignments contain alignments with over 200,000 sequences. New technology in DNA sequencing is enabling sequences to be determined faster than ever, so the total volume of sequence data available is doubling approximately once a year. However, sophisticated computer programs like Jalview require maintenance to fix bugs and to introduce new features as new techniques and data sources are developed world-wide. In order to ensure that Jalview can meet the needs of its large community in the face of the data onslaught, we are requesting support for staff to maintain and develop the Jalview Resource and train people how to use it. The principal aims of the resource will be: 1. to drive the maintenance and further development of the Jalview sequence analysis resource from October 2014 onwards. 2. To provide a range of training resources and regular workshops both for end-users of Jalview and for software developers who wish to add new features or incorporate Jalview in their own systems. 3. To facilitate the open development of Jalview as a community project. 4. To develop Jalview to be able to view, calculate properties of, and edit alignments of any size. 5. To migrate the Jalview applet that works on a web-page to Javascript. 6. To extend Jalview to provide flexible access to sophisticated state-of-the-art tools for sequence search and alignment in collaboration with their developers. 7. To extend Jalview to support state-of-the-art tools for the calculation of evolutionary trees. 8. To continue to seek new funding sources to expand the Jalview development team and improve the long-term sustainability of the resource. The applications of the jalview resource are many fold, from a teaching tool, though a figure-for-publication-making tool and expert analysts' workbench, to a neat way to display sequence alignments on a web page. The applications of Jalview span all areas of biology and so the benefits of the resource are legion.

比较是每个人日常生活的核心部分。如果两个物体看起来相似，那么第一个猜测是它们可能具有相似的功能。比较来自不同个体或物种的生物分子DNA、RNA和蛋白质是理解每个分子功能的核心。DNA、RNA和蛋白质分子可以被表示为几个字母组成的长词，长度可达数千个甚至数百万个字母。正是这些单词，或“序列”，通过计算机程序进行比较。例如，将植物致病细菌的蛋白质序列与植物的蛋白质序列进行比较，可能会为设计杀死细菌而不是植物的治疗方法提供建议。理想的情况是，同时比较两个以上的序列，这样可以更容易地发现共同特征。这一过程被称为“多序列比对”，是现代生物学中最强大的技术之一。易于使用但功能丰富的交互式计算机程序对于可视化和使大多数信息能够从多个序列比对中提取是必不可少的。Jalview是用于可视化和编辑序列比对的最广泛使用的程序。它安装在世界各地超过55,000台计算机上，在数十万个网页上，数千名科学家和学生每天都在使用它。Jalview不仅允许查看比对、着色和编辑比对，而且还利用互联网连接到1400多个序列来源和这些序列上的注释。此外，Jalview利用最先进的互联网技术连接到计算机服务器，这些服务器可以对序列执行大型计算，并在几秒钟或几分钟内将这些计算返回给用户。通过这种方式，该程序将大量人类知识放在科学家的指尖上，从而为他们节省了大量时间来探索他们最喜欢的蛋白质、DNA或RNA分子的功能。一些比对数据库包含超过200,000个序列的比对。DNA测序中的新技术使人们能够比以往任何时候都更快地确定序列，因此可用序列数据的总量大约每年翻一番。然而，像Jalview这样复杂的计算机程序需要维护来修复错误并引入新功能，因为世界各地都在开发新的技术和数据源。为了确保Jalview在面对数据冲击时能够满足其大型社区的需求，我们请求为员工提供支持，以维护和开发Jalview资源并培训人们如何使用它。该资源的主要目标是：1.从2014年10月起推动Jalview序列分析资源的维护和进一步开发。2.为Jalview的最终用户和希望增加新功能或将Jalview纳入其自身系统的软件开发人员提供一系列培训资源和定期讲习班。3.促进Jalview作为社区项目的开放发展。4.开发Jalview，使其能够查看、计算和编辑任意大小的路线。5.将在网页上工作的Jalview小程序移植到Java脚本。6.对Jalview进行扩展，以便与其开发人员合作，灵活访问先进的序列搜索和比对工具。7.扩展Jalview以支持最先进的进化树计算工具。8.继续寻求新的资金来源，以扩大Jalview开发团队，提高资源的长期可持续性。Jalview资源的应用有很多方面，从教学工具、出版插图制作工具和专家分析工作台，到在网页上显示序列比对的巧妙方式。Jalview的应用跨越了生物学的所有领域，因此该资源的好处是多种多样的。

项目成果

A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase.

• DOI: 10.1371/journal.pone.0184405
• 发表时间: 2017
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Britto-Borges T;Barton GJ
• 通讯作者: Barton GJ

A unified approach to evolutionary conservation and population constraint in protein domains highlights structural features and pathogenic sites

蛋白质领域进化保护和种群限制的统一方法突出了结构特征和致病位点

• DOI: 10.21203/rs.3.rs-3160340/v1
• 发表时间: 2023
• 作者: MacGowan S

Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics.

• DOI: 10.7554/elife.70658
• 发表时间: 2021-08-26
• 期刊: eLife
• 影响因子: 7.7
• 作者: Barton MI;MacGowan SA;Kutuzov MA;Dushek O;Barton GJ;van der Merwe PA
• 通讯作者: van der Merwe PA

Effects of common mutations in the SARS-CoV-2 Spike RBD domain and its ligand the human ACE2 receptor on binding affinity and kinetics

• DOI: 10.1101/2021.05.18.444646
• 发表时间: 2021-05
• 期刊: bioRxiv
• 作者: Michael I. MacGowan;Stuart Kutuzov;Mikhail Dushek;O. Barton;Geoffrey J. Merwe;P. Anton;Michael I. Barton;Stuart A. MacGowan;M. Kutuzov;Omer Dushek;G. Barton;A. V. D. Merwe

Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1.

• DOI: 10.15252/embj.201591593
• 发表时间: 2015-11-12
• 期刊: The EMBO journal
• 作者: Lai YC;Kondapalli C;Lehneck R;Procter JB;Dill BD;Woodroof HI;Gourlay R;Peggie M;Macartney TJ;Corti O;Corvol JC;Campbell DG;Itzen A;Trost M;Muqit MM
• 通讯作者: Muqit MM