PSC BIOMED ROADSHOW: WORKSHOP AT TENNESSEE STATE UNIVERSITY APRIL 6 & 7, 2006

PSC BIOMED 路演：4 月 6 日在田纳西州立大学举办的研讨会

• 批准号: 7601465
• 负责人: HUGH B NICHOLAS
• 金额: $ 0.03万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601465
• 关键词: Accounting; Algorithms; Bioinformatics; Biological; Biological Sciences; Blast Cell; Catalytic Domain; Coffee; Computer Retrieval of Information on Scientific Projects Database; Computer software; Computers; Consensus; Databases; Diagnostic; Educational process of instructing; Educational workshop; Foundations; Funding; Goals; Grant; Institution; Internet; Laboratories; Learning; Methods; Numbers; Participant; Pattern; Phylogeny; Protocols documentation; Research; Research Personnel; Resources; Sequence Alignment; Sequence Analysis; Services; Source; Specific qualifier value; Supercomputing; TPO gene; Techniques; Tennessee; Time; United States National Institutes of Health; Universities; Weight; base; biomedical resource; day; design; expectation; heuristics; lectures; markov model; programs; promoter; research study; supercomputer; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The Department of Biological Sciences at Tennessee State University and Pittsburgh Supercomputing Center's National Resource for Biomedical Supercomputing This two-day workshop is designed to teach researchers at Tennessee State University the basics of sequence analysis. Workshop participants will learn how to use tools for sequence analysis on the supercomputers at Pittsburgh Supercomputing Center (PSC). Lectures will be led by Alex Ropelewski, David Deerfield, and Hugh Nicholas. Computer laboratory sessions will follow each lecture. Each participant will receive an account at the PSC to allow them to experiment with the techniques described throughout the workshop. Each of the four topics described below will be covered in a lecture followed by a computer laboratory session: Bioinformatics and Sequence Analysis Resources on the Internet The advent of the Internet and the World Wide Web has substantially increased the availability of information and computational resources available to experimental biologists. This lecture will describe a number of online resources available, including resources and services availiable at the Pittsburgh Supercomputing Center. We will also discuss the use of the EMBOSS software and how to locate and retreive specified sequences from a sequence database. Database Searches and Pairwise Alignments This lecture presents both the mathematical and biological foundations of sequence comparison. That is, the lecture will describe in detail the various sequence alignment algorithms including the approximations made in the heuristics (e.g., FASTA and BLAST) to decrease computational time as opposed to searches with a rigorous algorithms (e.g., Needleman-Wunsch, Smith-Waterman). The lecture will also describe the underlying mathematical and biological bases for the similarity matrices in current use and how these tables should be properly used. The intended goal is to provide a researcher with the necessary background information about the search protocols so that they are assured of making good choices in their database searches and understand the shortcomings of naively using a database searching tool. Multiple Sequence Alignments This lecture covers aligning several sequences in their entirety (global alignments) and how global alignments are related to underlying biological phylogenies. During the lecture, we will describe the mathematical and biological basis for each of the multiple alignment programs and demonstrate the inherent weaknesses in each approach (e.g., ClustalW, MSA, or T-COFFEE). Discovering Diagnostic Patterns and Motifs in Unaligned Sequences Participants will be introduced to motifs and patterns and the various formats in which they are commonly represented, including consensus residues, regular expressions, hidden Markov Models and weight matrices. Discusses methods availiable to identify short, well conserved local patterns, such as promoter sequences or catalytic sites. Also discusses profile analysis and expectation maximization techniques. Participant Information: The local contact for this workshop is Dr. Terrance L. Johnson, Dept. of Biological Sciences, TSU, [e-mail], 615-963-5681.

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 田纳西州立大学生物科学系和匹兹堡超级计算中心生物医学超级计算国家资源 这个为期两天的研讨会旨在向田纳西州立大学的研究人员传授序列分析的基础知识。研讨会参与者将学习如何在匹兹堡超级计算中心(PSC)的超级计算机上使用工具进行序列分析。讲座将由Alex Ropelewski、David Deerfield和Hugh Nicholas主持。每堂课之后都会有计算机实验室课程。每个参与者都将在PSC收到一个帐户，以允许他们在整个研讨会中试验所述的技术。以下四个主题中的每一个都将在一堂课中讲述，然后是计算机实验室课程： 互联网上的生物信息学和序列分析资源 互联网和万维网的出现极大地增加了实验生物学家可获得的信息和计算资源。本讲座将介绍一些可用的在线资源，包括匹兹堡超级计算中心可用的资源和服务。我们还将讨论EMBOSS软件的使用以及如何从序列数据库中定位和检索指定的序列。 数据库搜索和成对比对 这堂课介绍了序列比较的数学和生物学基础。也就是说，讲座将详细描述各种序列比对算法，包括在启发式算法(例如，FASTA和BLAST)中进行的近似，以减少计算时间，而不是使用严格的算法(例如，Needleman-Wunsch，Smith-Waterman)进行搜索。本讲座还将介绍当前使用的相似性矩阵的基本数学和生物学基础，以及如何正确使用这些表。计划的目标是向研究人员提供关于搜索协议的必要背景信息，以便他们确信在数据库搜索中作出正确选择，并了解幼稚地使用数据库搜索工具的缺点。 多个序列比对 这堂课包括对几个序列的整体进行比对(全球比对)，以及全球比对如何与潜在的生物系统发育相关。在讲座中，我们将描述多种比对方案中每一种的数学和生物学基础，并演示每种方法的固有弱点(例如，CluastW、MSA或T-Cafee)。 发现未比对序列中的诊断模式和基序 将向学员介绍主题和模式及其常见的各种表示形式，包括共识残留物、正则表达式、隐马尔可夫模型和权重矩阵。讨论可用于识别短的、保守的局部模式的方法，例如启动子序列或催化位点。还讨论了简档分析和期望最大化技术。 参与者信息：本次研讨会的当地联系人是Terrance L.Johnson博士，系。生物科学系，TSU，[e-mail]，615-963-5681。