The Jalview Resource for Sequence Analysis and Annotation - www.jalview.org

用于序列分析和注释的 Jalview 资源 - www.jalview.org

• 批准号: BB/G022682/1
• 负责人: Geoffrey Barton
• 金额: $ 69.18万
• 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: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG022682%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. Likewise, 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 sequences of letters and it is these 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 generally agreed to be the most widely used program for visualising sequence alignments and editing them. It is installed on over 16,000 computers world-wide, on millions of web pages, and in daily use by thousands of scientists and students. Although other programs exist to visualise and edit multiple alignments, Jalview not only allows alignments to be viewed coloured and edited, but also exploits the internet to connect to over 70 sources of sequences and complex 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 sequence alignments contain alignments with over 70,000 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. Core funding for Jalview development ended in 2007, so 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 and training to maintain and develop the Jalview Resource. The principal aims of the resource will be: 1. To provide core support and maintenance. 2. To continue to drive Jalview development to meet the needs of new research techniques and data types through close interactions with the research groups at Dundee and elsewhere, and to add new features to Jalview to support visualisation and data analysis for services developed in the UK and rest of the World. 3. To facilitate the open development of Jalview as a community project by coordinating Jalview development by software developers in the community with needs for specific new features. 4. To provide extensive web-based user-documentation and programming guides for Jalview as well as regular training workshops both for end-users of Jalview and for developers who wish to add Jalview to their resources, or develop new features. 5. To seek out funding opportunities for new developments to Jalview above and beyond those possible with the resources requested in this application. 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中心部分。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。同样，比较来自不同个体或物种的生物分子DNA、RNA和蛋白质对于了解每个分子的作用至关重要。DNA、RNA和蛋白质分子可以用字母序列来表示，计算机程序就是对这些序列进行比较。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，可能会提出设计一种杀死细菌而不是植物的治疗方法的方法。理想情况下，同时比较两个以上的序列，因为这使得更容易发现共同特征。这个过程被称为“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是必不可少的可视化，并使大多数信息被提取多个序列比对。Jalview，通常被认为是最广泛使用的可视化序列比对和编辑它们的程序。它安装在全球16，000多台计算机上，数百万个网页上，并被数千名科学家和学生日常使用。虽然存在其他程序来可视化和编辑多个比对，但Jalview不仅允许对比对进行着色和编辑，而且还利用互联网连接到70多个序列源和这些序列上的复杂注释。此外，Jalview利用最先进的互联网技术连接到计算机服务器，可以对序列进行大型计算，并在几秒钟或几分钟内将这些数据返回给用户。通过这种方式，该程序将大量的人类知识放在科学家的指尖，从而为他们节省了大量的时间来探索他们最喜欢的蛋白质，DNA或RNA分子的功能。一些序列比对数据库包含超过70，000个序列的比对。DNA测序中的新技术使序列比以往任何时候都更快地确定，因此可用的序列数据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，并随着新技术和数据源在世界范围内的开发而引入新功能。Jalview开发的核心资金于2007年结束，因此，为了确保Jalview能够在面对数据冲击时满足其庞大社区的需求，我们正在请求支持员工和培训，以维护和开发Jalview资源。资源的主要目标是：1。提供核心支持和维护。2.通过与邓迪和其他地方的研究小组的密切互动，继续推动Jalview的发展，以满足新的研究技术和数据类型的需求，并为Jalview添加新功能，以支持在英国和世界其他地区开发的服务的可视化和数据分析。3.通过协调社区中的软件开发人员对Jalview的开发以及对特定新功能的需求，促进Jalview作为社区项目的开放开发。4.为Jalview提供广泛的基于Web的用户文档和编程指南，并为Jalview的最终用户和希望将Jalview添加到其资源或开发新功能的开发人员提供定期培训研讨会。5.为Jalview的新发展寻找资金机会，超越本申请所要求的资源。jalview资源的应用有很多方面，从教学工具，到出版物制作工具和专家分析工作台，再到在网页上显示序列比对的简洁方式。Jalview的应用涵盖了生物学的所有领域，因此该资源的好处很多。

项目成果

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

Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants.

• DOI: 10.1371/journal.pcbi.1009922
• 发表时间: 2022-03
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: MacGowan SA;Barton MI;Kutuzov M;Dushek O;van der Merwe PA;Barton GJ
• 通讯作者: Barton GJ

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

Visualization of Biomedical Data

生物医学数据可视化

• DOI: 10.7287/peerj.preprints.26896v1
• 发表时间: 2018
• 作者: O'Donoghue S