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Bacterial Bioinformatics

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Bacterial Bioinformatics

Instructor: Rebecca Wattam

24,319 already enrolled

8 modules

Gain insight into a topic and learn the fundamentals.

306 reviews

Intermediate level

Recommended experience

1 week to complete

at 10 hours a week

Flexible schedule

Learn at your own pace

8 modules

Gain insight into a topic and learn the fundamentals.

306 reviews

Intermediate level

Recommended experience

1 week to complete

at 10 hours a week

Flexible schedule

Learn at your own pace

What you'll 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

Skills you'll gain

Details to know

Assessments

8 assignments

Taught in English

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There are 8 modules in this course

This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses BV-BRC, the Bacterial and Viral Bioinformatics Resource Center (merger of PATRIC, IRD and ViPR, the three former resources), as the platform for analysis. BV-BRC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center, providing 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.

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. NOTE: The exercises in this course 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 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.

What's included

7 videos1 assignment

7 videosTotal 42 minutes

Instructor introduction4 minutes
History of BV-BRC and the BRC program4 minutes
BV-BRC overview - tabs and information17 minutes
Registering and logging on to BV-BRC3 minutes
PATRIC workspace-Create Shared Workspace7 minutes
Sharing a genome with other PATRIC users4 minutes
Copying a genome annotation job to a shared workspace4 minutes

1 assignmentTotal 30 minutes

PATRIC overview, login, and workspace sharing30 minutes

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.

What's included

7 videos1 assignment

7 videosTotal 49 minutes

Introduction to genome assembly7 minutes
Uploading read files to the workspace for assembly12 minutes
Submitting reads to the Genome Assembly Service8 minutes
Selecting assembly strategies and submitting the assembly job8 minutes
Monitoring the assembly job and reviewing job results7 minutes
Genome coverage in Genome Report2 minutes
Assembly questions and getting help with problems5 minutes

1 assignmentTotal 30 minutes

Review of genome assembly30 minutes

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.

What's included

7 videos1 assignment

7 videosTotal 77 minutes

Introduction to genome annotation in PATRIC5 minutes
Uploading contig files to the PATRIC workspace12 minutes
Submitting a job to the PATRIC Genome Annotation Service8 minutes
Reviewing the resulting Genome Report20 minutes
Downloading the generated files 11 minutes
Viewing your annotated genome in PATRIC15 minutes
Finding help or reporting problems with the service5 minutes

1 assignmentTotal 30 minutes

Review of genome annotation30 minutes

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.

What's included

10 videos1 assignment

10 videosTotal 101 minutes

Introduction to Comprehensive Genome Analysis in PATRIC2 minutes
Submitting a job using reads16 minutes
Submitting contigs8 minutes
Full Genome Report13 minutes
Job Results12 minutes
Assembly results12 minutes
Annotation results12 minutes
Viewing annotated genome12 minutes
Finding help and citing5 minutes
Hybrid Assembly Summary8 minutes

1 assignmentTotal 30 minutes

Review of the Comprehensive Genome Analysis Service30 minutes

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.

What's included

9 videos1 assignment

9 videosTotal 107 minutes

Introduction to codon trees3 minutes
Creating genome groups for building codon trees16 minutes
Submitting the tree-building job12 minutes
Reviewing the codon tree report12 minutes
Accessing codon tree files in the jobs folder10 minutes
Removing problem genomes from groups 18 minutes
Using the Protein Family Sorter to improve the tree16 minutes
Viewing the tree in FigTree9 minutes
Finding help and citing PATRIC11 minutes

1 assignmentTotal 30 minutes

Review of codon trees30 minutes

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.

What's included

4 videos1 assignment

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.

What's included

13 videos1 assignment

13 videosTotal 99 minutes

Introduction to Protein Family Sorter5 minutes
Using Global Search8 minutes
Creating a genome group5 minutes
Submitting a Protein Family Sorter Service analysis job6 minutes
Protein Family Sorter tabular results8 minutes
Filtering tabular results9 minutes
Heatmap filtering6 minutes
Heatmap clustering6 minutes
Anchoring and downloading heatmap data9 minutes
Using the Feature Table and Compare Region Viewer14 minutes
Downloading sequences from Feature Table and viewing in the Genome Browser11 minutes
BLASTing a genomic region11 minutes
Protein Family Sorter summary3 minutes

1 assignmentTotal 30 minutes

Review of Protein Family Sorter30 minutes

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.

What's included

11 videos1 assignment

11 videosTotal 74 minutes

Introduction to Proteome Comparison4 minutes
Selecting parameters9 minutes
Selecting a reference genome4 minutes
Using a feature group or FASTA file as input6 minutes
Using a feature group as the reference2 minutes
Using a FASTA file as the reference4 minutes
Selecting the genomes to use for the comparison3 minutes
3 flavors of reference genomes6 minutes
Reviewing the output job results21 minutes
Citing PATRIC and getting help5 minutes
Summary of analysis of two assembly strategies9 minutes

1 assignmentTotal 30 minutes

Review of Proteome Comparison30 minutes

Instructor

Instructor ratings

(118 ratings)

Rebecca Wattam

University of Virginia

1 Course24,319 learners

Offered by

University of Virginia

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Showing 3 of 306

Reviewed on Feb 6, 2024

It is really good...got to learn more about health informatics

Reviewed on Dec 23, 2020

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

Reviewed on Dec 4, 2022

It is a very good course to start to analyze biodata

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