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所在平台: Coursera |
课程主页: https://www.coursera.org/learn/informatics
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课程名称：细菌生物信息学 课程概述：本课程提供了关于细菌序列数据的常见基于基因组的分析任务的演示和练习。该课程使用PATRIC（病原体资源集成中心，PathoSystems Resource Integration Center）作为分析平台。PATRIC是由美国国立卫生研究院（NIH）和国家过敏和传染病研究所（NIAID）资助的细菌生物信息学资源中心，提供全面的细菌基因组数据以及集成的分析工具和可视化功能。此外，PATRIC还提供个人工作区，用户可以上传和分析自己的数据。课程参与者将掌握从原始序列数据开始进行细菌基因组比较分析所需的技能。第一模块的课程内容涵盖了基因组组装、注释、系统发育树构建以及蛋白质家族/蛋白质组比较。每节课在前一节的基础上进行构建，形成完整的基线分析工作流程。 课程大纲： 1. **简介**：介绍BV-BRC（细菌和病毒资源集成中心，前身为PATRIC），提供支持细菌研究的综合性生物信息学资源数据和分析工具。 2. **组装**：提供使用BV-BRC基因组组装服务从一组细菌序列读取中组装基因组的分步指导，并通过练习增强理解和熟练度。 3. **注释**：提供使用BV-BRC细菌基因组注释服务对组装好的基因组进行注释的分步指导，并通过练习提升用户的能力。 4. **综合基因组分析**：提供从细菌序列读取中组装、注释和执行自动化分析的分步指导，帮助用户熟练掌握服务的使用。 5. **基于密码子的系统发育树**：教用户如何生成基于密码子的系统发育树，并进行相关练习以增强理解。 6. **相似基因组查找器**：引导用户使用相似基因组查找服务定位与目标基因组相似的基因组及其分类。 7. **蛋白质家族排序器**：帮助用户使用BV-BRC蛋白质家族排序器比较一组基因组中蛋白质家庭的存在、缺失和计数。 8. **蛋白组比较**：教授用户如何使用BV-BRC蛋白组比较服务将一组基因组与参考基因组、特征组或FASTA文件进行比较。 本课程将为学习者提供进行细菌基因组比较分析所需的基本技能和实际操作经验。
Name:Introduction
Description:This lesson provides an introduction to BV-BRC, the Bacterial and Viral Resource Integration Center (formerly PATRIC), a Bioinformatics Resource Center dedicated to supporting bacterial research. BV-BRC provides comprehensive bacterial genomic data with integrated analysis tools and visualizations. BV-BRC also provides a private workspace where users can upload and analyze their own data. BV-BRC will serve as the platform for the analysis methods covered in this module. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.
Name:Assembly
Description:This lesson provides step-by-step instructions for assembling a genome from a set of bacterial sequence reads using the BV-BRC Genome Assembly Service. Exercises are included to enhance comprehension and build proficiency in using the assembly process. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.
Name:Annotation
Description:This lesson provides step-by-step instructions for annotating a genome from contigs using the BV-BRC Bacterial Genome Annotation Service. Exercises are included to enhance comprehension and build proficiency in using the annotation process. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.
Name:Comprehensive Genome Analysis
Description:This lesson provides step-by-step instructions for assembling, annotating, and performing an automated analysis of a genome from a set of bacterial sequence reads using the BV-BRC Comprehensive Genome Analysis Service. Exercises are included to enhance comprehension and build proficiency in using the service. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.
Name:Codon-Based Phyogenetic Trees
Description:This lesson provides step-by-step instructions for generating a codon-based phylogentic tree from a set of genomes using the BV-BRC Codon Tree Service. Exercises are included to enhance comprehension and build proficiency in using the service. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.
Name:Similar Genome Finder
Description:This lesson provides step-by-step instructions for finding genomes (and associated taxonomy) in BV-BRC similar to your genome or sequences using the Similar Genome Finder Service. Exercises are included to enhance comprehension and build proficiency in using the service. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.
Name:Protein Family Sorter
Description:This lesson provides step-by-step instructions for using the BV-BRC Protein Family Sorter to compare presence, absence, and counts of proteins in protein families across a set of genomes. Exercises are included to enhance comprehension and build proficiency in using the tool. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.
Name:Proteome Comparison
Description:This lesson provides step-by-step instructions for using the BV-BRC Proteome Comparison Service to compare a set of genomes against a reference genome, feature group, or FASTA file. Exercises are included to enhance comprehension and build proficiency in using the tool. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.
This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses PATRIC, the PathoSystems Resource Integration Center, as the platform for analysis. PATRIC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center, providing comprehensive bacterial genomic data with integrated analysis tools and visualizations. PATRIC also provides a private workspace where users can upload and analyze their own data. Course participants will gain skills needed to do comparative analysis of bacterial genomes, starting with raw sequence data.The lessons in the first module cover genome assembly, annotation, phylogenetic tree construction, and protein family / proteome comparisons. Each lesson builds on the previous, creating a complete baseline analysis workflow.
