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生物信息学I

Bioinformatics I
课程网址: https://ocw.vu.edu.pk/CourseDetails.aspx?cat=Bioinformatics&cours...  
主讲教师: Dr. Safee Ullah Choudhry
开课单位: 巴基斯坦虚拟大学
开课时间: 信息不详。欢迎您在右侧留言补充。
课程语种: 英语
中文简介:

生物信息学背景，生物信息学概论，对生物信息学的需求I，对生物信息学的需求II，生物信息学的应用I，生物信息学的应用II，生物信息学的前沿I，生物信息学的前沿II，课程内容概述I，课程概述内容II，课程内容概述III，基因，mRNA和蛋白质序列，转录，核苷酸，翻译，氨基酸，生物序列信息的存储，使用Entrez，使用Uniprot，比较序列，序列的相似性和差异，成对序列比对I ，成对序列比对II，成对序列比对III，点图，点图示例，同一性与相似性，比对介绍，方法，为什么要进行局部比对？ ，dels对齐，序列中的序列对齐，动态编程简介，动态编程要点，动态编程方法论，Needleman Wunsh算法I，Needleman Wunsh算法II，Needleman Wunsh算法III，Needleman Wunsh算法示例，回溯对齐，重新访问全局和局部比对，重叠比对，重叠比对的例子，从整体比对移至局部比对，Smith Waterman算法，Smith Waterman算法的例子，重复比对，重复比对的范例，针对全局，重叠，局部和重复比对的回溯策略的回顾，评分比对介绍，通过评分测量比对，评分矩阵，派生评分矩阵，PAM矩阵，BLOSSUM矩阵，多序列比对介绍，多序列比对的更多内容，MSA的逐步比对，MSA示例，CLUSTAL，BLAST I简介，BLAST II简介，BLAST算法，BLAST类型， BLAST摘要，FastA I简介，FastA II简介，FASTA算法，FASTA类型，FASTA摘要，生物学数据库和门户网站，实验，合奏，Uniprot，SwissProt，同源，同源和正论，序列比对，分子综述进化和系统发育，序列进化，算法和示例，引入UPGMA，UPGMA算法，求解示例，引入其他系统发生方法，最大简约性示例，DNA到RNA序列，碱基互补性，RNA类型及其功能，RNA的重要性结构，RNA折叠，折叠能量，折叠能量计算实例，RNA二级结构的类型I，RNA二级结构的类型II，RNA二级结构的类型III，RNA三次结构，RNA结构的圆形表示，RNA结构的实验方法确定RNA结构，RNA结构预测策略，RNA 2结构预测点图，基于能量的方法，Zuke r算法，Zuker算法示例，Zuker算法流程图，Martinez算法，动态编程方法，Nussinov Jacobson算法概述，NJ算法流程图，Jacobson示例算法，得分计算和追溯，算法比较，Web资源：RNA Bricks，Web资源：MFOLD ，从DNA / RNA序列到蛋白质，氨基酸编码，开放阅读框，ORF提取-流程图，测序蛋白质，MS在测序中的应用，MS蛋白质组学技术，基于MS的蛋白质组学类型，自下而上的蛋白质组学，两种方法自下而上的蛋白质组学，自上而下的蛋白质组学，蛋白质鉴定，蛋白质电离技术，MS1和完整蛋白质质量，计分完整蛋白质质量，蛋白质片段化技术，串联质谱，测量实验片段质量，计算理论片段质量，肽序列标签，提取肽序列标签，在蛋白质搜索中使用肽序列标签，对肽序列T评分ags，计算机蛋白质片段化，计算机片段比较和评分，蛋白质序列数据库搜索算法，综合评分方案，大规模蛋白质组学，蛋白质组学数据文件格式，RAW文件格式，MGF文件格式，开放式MS数据，格式，在线蛋白质组学工具吉祥物，在线蛋白质组学工具ProSight PTM，示例案例I，示例案例II，示例案例III，示例案例IV，示例案例V，示例案例VI，氨基酸I的特性，氨基酸II的特性，氨基酸特性III，氨基酸特性IV，氨基酸特性V，氨基酸结构特性I，氨基酸结构特性II，氨基酸结构特性III，氨基酸结构特性IV，蛋白质折叠介绍，蛋白质折叠的重要性，计算蛋白质折叠的可能性，蛋白质折叠的过程，蛋白质折叠的模型，蛋白质结构，主要，次要y，三级和四级结构，蛋白质的一级结构，蛋白质的二级结构I，蛋白质的二级结构，蛋白质的三级结构，蛋白质的第四级结构，蛋白质键角介绍，Ramachandran图，结构化可视化I，结构化可视化II ，蛋白质结构的实验确定，蛋白质数据库，可视化技术，蛋白质可视化的在线资源，蛋白质可视化的类型，蛋白质结构能量的介绍，蛋白质结构能量的计算，能量计算的结构确定，实验结构确定的回顾，蛋白质结构Alpha螺旋I，蛋白质结构Alpha螺旋II，蛋白质结构Beta板I，蛋白质结构Beta板II，蛋白质结构环I，蛋白质结构环II，蛋白质结构线圈，结构分类I，结构分类II，示例蛋白质域，CATH分类，分类数据库，结构分类算法，蛋白质结构比较，结构比较策略I，结构比较策略II，结构比较在线资源，蛋白质结构预测，二级结构预测，Chou Fasman算法简介， 2` Chou Fasman算法，Chou Fasman算法I，Chou Fasman算法II，Chou Fasman算法III，Chou Fasman算法IV，Chou Fasman算法–流程图I，Chou Fasman算法–流程图II，Chou Fasman算法–流程图III，Chou的结构Fasman算法-改进，可视化摘要，分类和预测，同源建模简介，同源建模需求，同源建模I的七个步骤，同源建模II的七个步骤，同源建模III的七个步骤III，算法和示例，折叠识别/线程I，折叠识别/线程II，折叠识别/线程化III，用于折叠识别的在线工具，iTASSER，GOR算法，3D 1D Bowie算法，3D 1D算法示例，用于结构的机器学习方法，预测，用于结构预测的神经网络，神经网络入门I，神经网络入门网络II，神经网络在结构预测中的应用，PSIPRED，隐马尔可夫模型介绍，隐马尔可夫模型在结构预测中的应用，从头算建模，Hinds和Levitt算法，HL算法示例，结构预测计算评估（CASP） ，同源性建模概述，用于同源性建模的在线工具，用于结构建模的数据库，SWISS模型，结构建模的回顾，丙型肝炎病毒基因型3A建模I的示例，丙型肝炎病毒基因型3A建模II的示例

课程简介: Background of Bioinformatics, Introduction to Bioinforamtics, Need for Bioinformatics - I, Need for Bioinformatics - II, Applications of Bioinformatics - I, Applications of Bioinformatics - II,Frontiers in Bioinformatics - I, Frontiers in Bioinformatics - II, Overview of Course Contents - I, Overview of Course Contents - II, Overview of Course Contents - III, Gene, mRNA and Protein Sequences,Transcription, Nucleotides, Translation, Amino Acids, Storage of Biological Sequence Information,Using Entrez,Using Uniprot,Comparing Sequences,Similarities and Differences in Sequences, Pairwise Sequence Alignment-I, Pairwise Sequence Alignment-II, Pairwise Sequence Alignment-III, Dot Plots, Example of Dot Plots, Identity vs. Similarity, Introduction to Alignment, Approaches, Why local alignments? ,Aligning In-dels, Aligning Mutations in Sequences,, Introduction to Dynamic Programming, Dynamic Programming - Essentials, Dynamic Programming Methodology, Needleman Wunsh Algorithm-I, Needleman Wunsh Algorithm-II, Needleman Wunsh Algorithm-III, Needleman Wunsh Algorithm-Example, Backtracking Alignments ,Revisiting Global and Local Alignments ,Overlap Matches ,Example of Overlap Matches, Moving From global to local alignment, Smith Waterman Algorithm, Example of Smith Waterman Algorithm, Repeated Alignments, Exmaple of repeated alignment, Review of Traceback Strategies for Global, Overlap, Local and Repeated Alignments, Introduction to Scoring Alignments,, Measuring alignments by scoring, Scoring matrices, Deriving scoring matrices, PAM Matrices, BLOSSUM Matrices, Introduction to Multiple Sequences Alignment, More on Multiple Sequence Alignment, Progressive Alignment for MSA, MSA Example, CLUSTAL, Introduction to BLAST - I, Introduction to BLAST - II, BLAST Algorithm, Types of BLAST ,Summary of BLAST, Introduction to FastA-I, Introduction to FastA-II, FASTA Algorithm, Types of FASTA, Summary of FASTA, Biological Databases and Portals, Expasy, Ensemble, Uniprot, SwissProt, Homology, Paralogy and Orthology, Review of Sequence Alignment, Molecular evolution and phylogeny, Evolution of sequences, Algorithm and examples, Introduce UPGMA, UPGMA Algorithm, Solve an example, Introduce other Phylogenetic Methods, Examples of Maximum Parsimony, DNA to RNA Sequences, Base Complementarity, Types of RNA and their Function, Significance of RNA Structures, RNA Folding, Energies of Folding, Calculating Energies of Folding - An Example, Types of RNA Secondary Structures - I, Types of RNA Secondary Structures - II, Types of RNA Secondary Structures - III, RNA Tertiary Structures, Circular Representation of RNA Structures, Experimental Methods for Determining RNA Strucutres, Strategies for RNA Structure Prediction, Dot Plots for RNA 2` Structure Prediction, Energy Based Methods, Zuker Algorithm, Example - Zuker Algorithm, Zuker Algorithm - Flowchart, Martinez Algorithm, Dynamic Programming Approaches, Nussinov -Jacobson Algorithm Overview, NJ Algorithm Flowchart, Example - Jacobson Algorithm, Score Calculations and Traceback, Comparison of Algorithms, Web Resources: RNA Bricks, Web resources: MFOLD, From DNA/RNA Sequences to Proteins, Coding of Amino Acids, Open Reading Frames, ORF Extraction – A Flowchart, Sequencing Proteins, Application of MS in sequencing, Techniques for MS Proteomics, Types of MS-based proteomics, Bottom Up Proteomics, Two Approaches for Bottom Up Proteomics, Top Down Proteomics, Protein Identification, Protein Ionization Techniques, MS1 and Intact Protein Mass, Scoring Intact Protein Mass, Protein Fragmentation Techniques, Tandem MS, Measuring Experimental Fragment`s Mass, Calculating Theoretical Fragment`s Mass, Peptide Sequence Tags, Extracting Peptide Sequence Tags, Using Peptide Sequence Tags in Protein Search, Scoring Peptide Sequence Tags, In silico Protein Fragmentation, In silico Fragment Comparison and Scoring, Protein Sequence Database Search Algorithm, Integrative Scoring Schemes, Large Scale Proteomics, Proteomics Data File Formats, RAW File Format, MGF File Format, Open MS Data, Formats, Online Proteomics Tools - Mascot, Online Proteomics Tools - ProSight PTM, Example Case Study - I, Example Case Study - II, Example Case Study - III, Example Case Study - IV, Example Case Study - V, Example Case Study - VI, Properties of Amino Acids - I, Properties of Amino Acids - II, Properties of Amino Acids - III, Properties of Amino Acids - IV, Properties of Amino Acids - V, Structural Traits of Amino Acids - I, Structural Traits of Amino Acids - II, Structural Traits of Amino Acids - III, Structural Traits of Amino Acids - IV, Introduction to Protein Folding, Importance of Protein Folding, Computing Protein Folding Possibilities, Process of Protein Folding, Models of Protein Folding, Protein Structures, Primary, Secondary, Tertiary and Quaternary Structures, Primary Structure of Proteins, Secondary Structures of Proteins - I, Secondary Structures of Proteins -II, Tertiary Structures of Proteins, Quaternary Structures of Proteins, Introduction to Protein Bond Angles, Ramachandran Plot, Structure Visualization - I, Structure Visualization - II, Experimental Determination of Protein Structure, Protein Data Bank, Visualization Techniques, Online Resources for Protein Visualization, Types of Protein Visualizations, Introduction to Energy of Protein Structures, Calculating Energies of Protein Structures, Structure Determination for Energy Calculations, Review of Experimental Structure Determination, Protein Structures - Alpha Helices I, Protein Structures - Alpha Helices II, Protein Structures - Beta Sheets I, Protein Structures - Beta Sheets II, Protein Structures - Loops I, Protein Structures - Loops II, Protein Structures - Coils,  Structure Classification - I,  Structure Classification - II, Examples of Protein Domains, CATH Classification, Classification Databases, Algorithms for Structure Classification, Protein Structure Comparison, Strategies for Structure Comparison - I, Strategies for Structure Comparison - II, Online Resources for Structure Comparison, Protein Structure Prediction, Predicting Secondary Structures, Introduction to Chou Fasman Algorithm, 2` Structures in Chou Fasman Algorithm, Chou Fasman Algorithm - I, Chou Fasman Algorithm - II, Chou Fasman Algorithm - III, Chou Fasman Algorithm - IV, Chou Fasman Algorithm – Flowchart I, Chou Fasman Algorithm – Flowchart II, Chou Fasman Algorithm – Flowchart III, Chou Fasman Algorithm – Improvements, Summary of Visualization, Classification and Prediction, Introduction to Homology modelling, Need for Homology Modelling, Seven Steps to Homology Modelling - I, Seven Steps to Homology Modelling - II, Seven Steps to Homology Modelling - III, Algorithm And Examples, Fold Recognition/Threading I, Fold Recognition/Threading II, Fold Recognition/Threading III, Online Tools for Fold Recognition, iTASSER, GOR Algorithm, 3D-1D Bowie Algorithm, Example of 3D-1D Algorithm, Machine Learning Approaches to Structure, Prediction, Neural Networks for Structure Prediction, Introduction to Neural Networks I, Introduction to Neural Networks II, Application of Neural Networks for Structure Prediction, PSIPRED, Introduction to Hidden Markov Models, Application of Hidden Markov Models to Structure Prediction, Ab initio modelling, Hinds and Levitt Algorithm, Example of HL Algorithm, Computational Assesment of Structure Prediction (CASP), Summary of Homology Modelling, Online Tools for Homology Modelling, Databases for Structure Modelling, SWISS MODEL, Review of Structure Modelling, Example of Hepatitis C Virus genotype 3A Modelling - I, Example of Hepatitis C Virus genotype 3A Modelling - II
关 键 词: 生物信息学; 应用; 课程
课程来源: 巴基斯坦虚拟大学公开课
数据采集: 2021-04-20：nkq
最后编审: 2021-04-20：nkq
阅读次数: 99

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