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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Intermediate Level

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

Approx. 14 hours to complete

English

Subtitles: French, Portuguese (European), Russian, English, Spanish

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

Shareable Certificate

Earn a Certificate upon completion

100% online

Start instantly and learn at your own schedule.

Flexible deadlines

Reset deadlines in accordance to your schedule.

Intermediate Level

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

Approx. 14 hours to complete

English

Subtitles: French, Portuguese (European), Russian, English, Spanish

Instructor

Rebecca Wattam

Professor

Biocomplexity Institute and Initiative

1,249 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.

Syllabus - What you will learn from this course

Week

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)

7 videos

Instructor introduction3m

History of PATRIC and the BRC program3m

PATRIC overview - tabs and information16m

Registering and logging on to PATRIC2m

PATRIC workspace-Create Shared Workspace6m

Sharing a genome with other PATRIC users4m

Copying a genome annotation job to a shared workspace3m

1 practice exercise

PATRIC overview, login, and workspace sharing30m

Week

Week 2

1 hour to complete

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.

1 hour to complete

7 videos (Total 49 min)

7 videos

Introduction to genome assembly6m

Uploading read files to the workspace for assembly11m

Submitting reads to the Genome Assembly Service8m

Selecting assembly strategies and submitting the assembly job8m

Monitoring the assembly job and reviewing job results7m

Genome coverage in Genome Report2m

Assembly questions and getting help with problems4m

1 practice exercise

Review of genome assembly30m

Week

Week 3

2 hours to complete

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.

2 hours to complete

7 videos (Total 77 min)

7 videos

Introduction to genome annotation in PATRIC5m

Uploading contig files to the PATRIC workspace12m

Submitting a job to the PATRIC Genome Annotation Service7m

Reviewing the resulting Genome Report19m

Downloading the generated files 11m

Viewing your annotated genome in PATRIC15m

Finding help or reporting problems with the service5m

1 practice exercise

Review of genome annotation30m

Week

Week 4

2 hours to complete

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.

2 hours to complete

10 videos (Total 101 min)

10 videos

Introduction to Comprehensive Genome Analysis in PATRIC2m

Submitting a job using reads16m

Submitting contigs8m

Full Genome Report13m

Job Results11m

Assembly results11m

Annotation results12m

Viewing annotated genome12m

Finding help and citing5m

Hybrid Assembly Summary8m

1 practice exercise

Review of the Comprehensive Genome Analysis Service30m

Week

Week 5

2 hours to complete

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.

2 hours to complete

9 videos (Total 107 min)

9 videos

Introduction to codon trees2m

Creating genome groups for building codon trees16m

Submitting the tree-building job11m

Reviewing the codon tree report11m

Accessing codon tree files in the jobs folder10m

Removing problem genomes from groups 17m

Using the Protein Family Sorter to improve the tree16m

Viewing the tree in FigTree8m

Finding help and citing PATRIC11m

1 practice exercise

Review of codon trees30m

Week

Week 6

1 hour to complete

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.

1 hour to complete

4 videos (Total 25 min)

4 videos

Launching a search using a genome7m

Launching a search using a contig file5m

Launching a search using a fastq file7m

Finding help and citing PATRIC3m

1 practice exercise

Review of Similar Genome Finder30m

Week

Week 7

2 hours to complete

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.

2 hours to complete

13 videos (Total 99 min)

13 videos

Introduction to Protein Family Sorter4m

Using Global Search7m

Creating a genome group5m

Submitting a Protein Family Sorter Service analysis job6m

Protein Family Sorter tabular results7m

Filtering tabular results8m

Heatmap filtering5m

Heatmap clustering5m

Anchoring and downloading heatmap data8m

Using the Feature Table and Compare Region Viewer14m

Downloading sequences from Feature Table and viewing in the Genome Browser11m

BLASTing a genomic region10m

Protein Family Sorter summary2m

1 practice exercise

Review of Protein Family Sorter30m

Week

Week 8

2 hours to complete

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.

2 hours to complete

11 videos (Total 74 min)

11 videos

Introduction to Proteome Comparison4m

Selecting parameters8m

Selecting a reference genome3m

Using a feature group or FASTA file as input6m

Using a feature group as the reference2m

Using a FASTA file as the reference4m

Selecting the genomes to use for the comparison3m

3 flavors of reference genomes5m

Reviewing the output job results21m

Citing PATRIC and getting help5m

Summary of analysis of two assembly strategies8m

1 practice exercise

Review of Proteome Comparison30m

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Bacterial Bioinformatics

Bacterial Bioinformatics