4.8
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24 個評分
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7 條評論

Rebecca Wattam

2,796 人已註冊

提供方

Bacterial Bioinformatics

弗吉尼亚大学

課程信息

11,011 次近期查看

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.

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100% 在線

立即開始，按照自己的計劃學習。

中級

This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.

完成時間大約為14 小時

英語（English）

字幕：法語（French）, （歐洲人講的）葡萄牙語, 俄語（Russian）, 英語（English）, 西班牙語（Spanish）

您將學到的內容有

Learn how to assemble a bacterial genome

Learn how to annotate a bacterial genome

Learn how to generate a phylogenetic tree from a set of bacterial genomes

Learn how to perform basic comparative analyses of a set of bacterial genomes

可靈活調整截止日期

根據您的日程表重置截止日期。

100% 在線

立即開始，按照自己的計劃學習。

中級

This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.

完成時間大約為14 小時

英語（English）

字幕：法語（French）, （歐洲人講的）葡萄牙語, 俄語（Russian）, 英語（English）, 西班牙語（Spanish）

講師

授課教師評分

4.78/5 （15 個評分）

Rebecca Wattam

Professor

Biocomplexity Institute and Initiative

2,796 個學生

1 門課程

提供方

弗吉尼亚大学

A premier institution of higher education, The University of Virginia offers outstanding academics, world-class faculty, and an inspiring, supportive environment. Founded by Thomas Jefferson in 1819, the University is guided by his vision of discovery, innovation, and development of the full potential of students from all walks of life. Through these courses, global learners have an opportunity to study with renowned scholars and thought leaders.

教學大綱 - 您將從這門課程中學到什麼

週

週 1

完成時間為 1 小時

Introduction

This lesson provides an introduction to PATRIC, the PathoSystems Resource Integration Center, a Bioinformatics Resource Center dedicated to supporting bacterial research. PATRIC provides 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. PATRIC will serve as the platform for the analysis methods covered in this module.

完成時間為 1 小時

7 個視頻（總計 42 分鐘）

週

週 2

完成時間為 1 小時

Assembly

This lesson provides step-by-step instructions for assembling a genome from a set of bacterial sequence reads using the PATRIC Genome Assembly Service. Exercises are included to enhance comprehension and build proficiency in using the assembly process.

完成時間為 1 小時

7 個視頻（總計 49 分鐘）

7 個視頻

Introduction to genome assembly6分鐘

Uploading read files to the workspace for assembly11分鐘

Submitting reads to the Genome Assembly Service8分鐘

Selecting assembly strategies and submitting the assembly job8分鐘

Monitoring the assembly job and reviewing job results7分鐘

Genome coverage in Genome Report2分鐘

Assembly questions and getting help with problems4分鐘

1 個練習

Review of genome assembly30分鐘

週

週 3

完成時間為 2 小時

Annotation

This lesson provides step-by-step instructions for annotating a genome from contigs using the PATRIC Genome Annotation Service. Exercises are included to enhance comprehension and build proficiency in using the annotation process.

完成時間為 2 小時

7 個視頻（總計 77 分鐘）

7 個視頻

Introduction to genome annotation in PATRIC5分鐘

Uploading contig files to the PATRIC workspace12分鐘

Submitting a job to the PATRIC Genome Annotation Service7分鐘

Reviewing the resulting Genome Report19分鐘

Downloading the generated files 11分鐘

Viewing your annotated genome in PATRIC15分鐘

Finding help or reporting problems with the service5分鐘

1 個練習

Review of genome annotation30分鐘

週

週 4

完成時間為 2 小時

Comprehensive Genome Analysis

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 PATRIC Comprehensive Genome Analysis Service. Exercises are included to enhance comprehension and build proficiency in using the service.

完成時間為 2 小時

10 個視頻（總計 101 分鐘）

週

週 5

完成時間為 2 小時

Codon-Based Phyogenetic Trees

This lesson provides step-by-step instructions for generating a codon-based phylogentic tree from a set of genomes using the PATRIC Codon Tree Service. Exercises are included to enhance comprehension and build proficiency in using the service.

完成時間為 2 小時

9 個視頻（總計 107 分鐘）

9 個視頻

Introduction to codon trees2分鐘

Creating genome groups for building codon trees16分鐘

Submitting the tree-building job11分鐘

Reviewing the codon tree report11分鐘

Accessing codon tree files in the jobs folder10分鐘

Removing problem genomes from groups 17分鐘

Using the Protein Family Sorter to improve the tree16分鐘

Viewing the tree in FigTree8分鐘

Finding help and citing PATRIC11分鐘

1 個練習

Review of codon trees30分鐘

週

週 6

完成時間為 1 小時

Similar Genome Finder

This lesson provides step-by-step instructions for finding genomes (and associated taxonomy) in PATRIC 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.

完成時間為 1 小時

4 個視頻（總計 25 分鐘）

週

週 7

完成時間為 2 小時

Protein Family Sorter

This lesson provides step-by-step instructions for using the PATRIC 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.

完成時間為 2 小時

13 個視頻（總計 99 分鐘）

13 個視頻

Introduction to Protein Family Sorter4分鐘

Using Global Search7分鐘

Creating a genome group5分鐘

Submitting a Protein Family Sorter Service analysis job6分鐘

Protein Family Sorter tabular results7分鐘

Filtering tabular results8分鐘

Heatmap filtering5分鐘

Heatmap clustering5分鐘

Anchoring and downloading heatmap data8分鐘

Using the Feature Table and Compare Region Viewer14分鐘

Downloading sequences from Feature Table and viewing in the Genome Browser11分鐘

BLASTing a genomic region10分鐘

Protein Family Sorter summary2分鐘

1 個練習

Review of Protein Family Sorter30分鐘

週

週 8

完成時間為 2 小時

Proteome Comparison

This lesson provides step-by-step instructions for using the PATRIC 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.

完成時間為 2 小時

11 個視頻（總計 74 分鐘）

11 個視頻

Introduction to Proteome Comparison4分鐘

Selecting parameters8分鐘

Selecting a reference genome3分鐘

Using a feature group or FASTA file as input6分鐘

Using a feature group as the reference2分鐘

Using a FASTA file as the reference4分鐘

Selecting the genomes to use for the comparison3分鐘

3 flavors of reference genomes5分鐘

Reviewing the output job results21分鐘

Citing PATRIC and getting help5分鐘

Summary of analysis of two assembly strategies8分鐘

1 個練習

Review of Proteome Comparison30分鐘

審閱

4.8

7 條評論

5 stars
83.33%
4 stars
12.50%
3 stars
4.16%

來自BACTERIAL BIOINFORMATICS的熱門評論

由 PP 提供2020年12月23日

very useful course , can solve a lot of problem in bacterium genome analysis easily

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Bacterial Bioinformatics

Bacterial Bioinformatics