4.7
stars
113 ratings

Rebecca Wattam

10,151 already enrolled

Offered By

Bacterial Bioinformatics

University of Virginia

About this Course

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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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Coursera Labs

Includes hands on learning projects.

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Intermediate Level

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

Approx. 13 hours to complete

English

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What you will learn

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

Flexible deadlines

Reset deadlines in accordance to your schedule.

100% online

Start instantly and learn at your own schedule.

Coursera Labs

Includes hands on learning projects.

Learn more about Coursera Labs

Intermediate Level

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

Approx. 13 hours to complete

English

Could your company benefit from training employees on in-demand skills?

Try Coursera for Business

Instructor

Instructor rating

4.75/5 (49 Ratings)

Rebecca Wattam

Professor

Biocomplexity Institute and Initiative

10,151 Learners

1 Course

Offered by

University of Virginia

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.

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Syllabus - What you will learn from this course

Week1

Week 1

1 hour to complete

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.

1 hour to complete

7 videos (Total 42 min)

Week2

Week 2

1 hour to complete

Assembly

1 hour to complete

7 videos (Total 49 min)

Week3

Week 3

2 hours to complete

Annotation

2 hours to complete

7 videos (Total 77 min)

Week4

Week 4

2 hours to complete

Comprehensive Genome Analysis

2 hours to complete

10 videos (Total 101 min)

Week5

Week 5

2 hours to complete

Codon-Based Phyogenetic Trees

2 hours to complete

9 videos (Total 107 min)

9 videos

Introduction to codon trees2mCreating genome groups for building codon trees16mSubmitting the tree-building job11mReviewing the codon tree report11mAccessing codon tree files in the jobs folder10mRemoving problem genomes from groups 17mUsing the Protein Family Sorter to improve the tree16mViewing the tree in FigTree8m Finding help and citing PATRIC11m

1 practice exercise

Review of codon trees30m

Week6

Week 6

1 hour to complete

Similar Genome Finder

1 hour to complete

4 videos (Total 25 min)

Week7

Week 7

2 hours to complete

Protein Family Sorter

2 hours to complete

13 videos (Total 99 min)

13 videos

Introduction to Protein Family Sorter4mUsing Global Search7mCreating a genome group5mSubmitting a Protein Family Sorter Service analysis job6mProtein Family Sorter tabular results7mFiltering tabular results8mHeatmap filtering5mHeatmap clustering5mAnchoring and downloading heatmap data8mUsing the Feature Table and Compare Region Viewer14mDownloading sequences from Feature Table and viewing in the Genome Browser11mBLASTing a genomic region10mProtein Family Sorter summary2m

1 practice exercise

Review of Protein Family Sorter30m

Week8

Week 8

2 hours to complete

Proteome Comparison

2 hours to complete

11 videos (Total 74 min)

11 videos

Introduction to Proteome Comparison4mSelecting parameters8mSelecting a reference genome3mUsing a feature group or FASTA file as input6mUsing a feature group as the reference2mUsing a FASTA file as the reference4mSelecting the genomes to use for the comparison3m3 flavors of reference genomes5mReviewing the output job results21mCiting PATRIC and getting help5mSummary of analysis of two assembly strategies8m

1 practice exercise

Review of Proteome Comparison30m

Reviews

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26 reviews

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3 stars
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TOP REVIEWS FROM BACTERIAL BIOINFORMATICS

by YSOct 27, 2022

Very informative course content and I have learned a lot

by GTFeb 4, 2022

i appreciate the dedication and design of the course. it so practical and friendly. thank You Dr. Rebecca.

by DRApr 28, 2022

It was great learning course. I learned so many new things from course

by WHDec 20, 2021

I appreciate the instructors for this amazing course that sharpen my skills in the bacterial genome analysis.

View all reviews

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Bacterial Bioinformatics

Bacterial Bioinformatics

About this Course

What you will learn