Computational Intelligence and Applications in Bioinformatics

计算智能及其在生物信息学中的应用

• 批准号: 238298-2013
• 负责人: Wiese, Kay
• 金额: $ 1.46万
• 依托单位: Simon Fraser University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=570389
• 关键词: Computational; Intelligence; Applications; Bioinformatics

Structure prediction of bio-molecules such as RNA and proteins is an important topic in Computational Biology. The structure is often determining the function of the molecule and can also be used to infer genetic origins (phylogeny). This research program focuses primarily on the following two objectives: 1) To develop improved algorithms for structure prediction of bio-molecules, particularly RNA. This is an important topic as more and more functional RNAs are discovered. 2) To develop improved visualization techniques, particularly for RNA visualization. For objective 1) the starting point will be the algorithm RnaPredict, developed in my lab and based on evolutionary computation. RnaPredict uses a number of advanced operators and representations. I plan to further evaluate, improve, and extend RnaPredict, particularly in the area of modeling non-canonical base pairs and the prediction of pseudoknots. The starting point for objective 2) will be jViz.Rna, a visualization tool for RNA secondary structure which has a number of benefits over existing tools, including: wide support of input and output formats, ability to produce high quality graphics for reproduction, interactive output for further manipulation by the end user, ability to display pseudoknots in a classical structure plot, and the ability to overlay two different structures for comparison. jViz.Rna also produces quantitative and qualitative comparisons between two structures. One particular challenge of RNA visualization is the the handling of pseudoknots. Most existing tools either do not model them in a traditional structure plot or do a relatively poor job. I plan to extend jViz.Rna to incorporate various topological tools to display more classes of pseudoknots in a planar way. This will also have potential benefits for the visualization community at large.

RNA、蛋白质等生物分子的结构预测是计算生物学中的一个重要课题。结构通常决定分子的功能，也可用于推断遗传起源（遗传学）。该研究计划主要侧重于以下两个目标： 1)开发生物分子结构预测的改进算法，特别是RNA。这是一个重要的课题，因为越来越多的功能RNA被发现。 2)开发改进的可视化技术，特别是RNA可视化。 对于目标1），起点将是我的实验室开发的基于进化计算的算法RnaPredict。RnaPredict使用了许多高级运算符和表示。我计划进一步评估、改进和扩展RnaPredict，特别是在非规范碱基对建模和伪结预测方面。 目标2）的起点将是jViz.Rna，这是一种RNA二级结构的可视化工具，与现有工具相比具有许多优点，包括：广泛支持输入和输出格式，能够产生高质量的图形供再现，交互式输出供最终用户进一步操作，能够在经典结构图中显示伪结，以及覆盖两个不同结构用于比较的能力。RNA还产生两种结构之间的定量和定性比较。RNA可视化的一个特殊挑战是伪结的处理。大多数现有的工具要么没有在传统的结构图中对它们进行建模，要么做得相对较差。我计划扩展jViz.rna以合并各种拓扑工具，从而以平面方式显示更多类的伪结。这也将为整个可视化社区带来潜在的好处。