SEA-PHAGES | Videos

SEA-PHAGES Videos

Channels

Tutorials (56 videos) Go to channel page

How-to videos that help with various parts of running or participating in a SEA-PHAGES course.

Subchannels

Genome Annotation (24 videos) Go to channel page

Tutorials that describe how to annotate a phage genome.

Subchannels

DNA Master (15 videos) Go to channel page

Tutorials that demonstrate how to use DNA Master to create high-quality phage genome annotations.

Videos

1. DNA Master: Setting Preferences

2. DNA Master: How to Auto-Annotate a Phage Genome

3. DNA Master: BLAST All Genes, or Just One

4. DNA Master: BLAST a Subset of Genes

5. DNA Master: How to Add, Delete, or Modify a Gene

6. DNA Master: Database and Documentation: How to Post, Recreate, and Parse

7. DNA Master: Checking Gaps in an Annotation

8. DNA Master: How to Annotate a +1 Translational Frameshift

9. DNA Master: How to Annotate a -1 Translational Frameshift

10. DNA Master: Merging Files

11. DNA Master: How to Validate and Renumber Genes

12. DNA Master: Minimal File Formatting

13. DNA Master: Fixing a Corrupted File

14. DNA Master: Submit a Final Annotation at PhagesDB

15. DNA Master: Review to Improve

Data Collection and Interpretation (9 videos) Go to channel page

Tutorials on how to collect and interpret data that is essential to produce a high-quality genome annotation.

Videos

Using PhagesDB to Support Genome Annotation

Using Phamerator to Explore Comparative Phage Genomics

Generating GeneMark Output

Interpreting GeneMarkS Output

Using tRNAscan-SE to Find tRNA Genes in Phage Genomes

Using Aragorn to Find tRNA Genes in Phage Genomes

Interpreting HHpred Results

Interpreting Starterator Output

Essential Functions and Cluster-Specific Forums

Phage Discovery: Overview (10 videos) Go to channel page

Videos that provide overviews for the various stages of Phage Discovery

Videos

Phage Discovery Overview: Virus

Phage Discovery Overview: Virus Replication

Phage Discovery Overview: Isolation

Phage Discovery Overview: Plaque Assay

Phage Discovery Overview: Purification

Phage Discovery Overview: Amplification

Phage Discovery Overview: Spot Test

Phage Discovery Overview: DNA Extraction

Phage Discovery Overview: Calculating a Titer

Phage Discovery Overview: Making Webbed Plates

Phage Discovery: Protocols (8 videos) Go to channel page

Tutorials for the basic wet-lab work of discovering phages.

Videos

1. Phage Discovery Protocol: Direct Isolation

2. Phage Discovery Protocol: Enriched Isolation

3. Phage Discovery Protocol: Plaque Assay

4. Phage Discovery Protocol: Picking a Plaque

5. Phage Discovery Protocol: Spot Test

6. Phage Discovery Protocol: Serial Dilution

7. Phage Discovery Protocol: Collecting Plate Lysate

8. Phage Discovery Protocol: DNA Extraction

Phage Discovery Prep Guide (5 videos) Go to channel page

Tutorials for the basic preparation of reagents and cultures for Phage Discovery.

Videos

1. Phage Discovery Prep: Filter-Sterilizing Solutions

2. Phage Discovery Prep: Liquid Culture

3. Phage Discovery Prep: Bacteria Streak Plate

4. Phage Discovery Prep: Glycerol Stocks

5. Phage Discovery Prep: Preparing Agar Plates

Comparative Genomics (6 videos) Go to channel page

Videos that demonstrate several ways to use comparative genomes to analyze groups of phage genomes.

Videos

1. Making Publication-Quality Phamerator Maps

2. Using the DNA Master Genome Manager

3. Using Genome Comparison Tools in DNA Master

4. How to use Gepard to Make Dotplots of Phage Genomes

5. Using PhamNexus to Create Nexus Files for SplitsTree

6. How to Make a SplitsTree Diagram for Phage Genomes

Assembly and QC (1 video) Go to channel page

Tutorials that demonstrate how to assemble and finish phage genomes after they've been sequenced.

Videos

1. Assembling Reads with Newbler

Classroom Tools (1 video) Go to channel page

Tutorials for various tools that can be used in a SEA-PHAGES classroom.

Videos

Using the Phage Enzyme Tools to Predict Cluster

Genome Announcements (1 video) Go to channel page

Tutorials designed to help write high-quality papers for the journal Genome Announcements.

Videos

1. Genome Announcements: General Content, Structure, and Format

Promotional (6 videos) Go to channel page

Videos that showcase the SEA-PHAGES program.

Videos

Interviews with K-RITH Students from the 2016 Mycobacterial Genetics Course

Welcome to SEA-PHAGES 2020

Students: What's the coolest part of the SEA-PHAGES course?

Students: What can you do now that you couldn't do before?

Students: How did the SEA-PHAGES course change your opinions about science?

An Introduction to SEA-PHAGES

2015 Symposium (20 videos) Go to channel page

Videos from the 7th Annual SEA-PHAGES Symposium, held at Janelia Research Campus in Ashburn, Virginia.

Videos

2015 Symposium: Dr. Eric Betzig's Keynote Talk

Graham Hatfull's Keynote Address at the 2015 SEA-PHAGES Symposium

Subchannels

2015 Student Talks (18 videos) Go to channel page

The student talks from the 2015 Symposium.

Videos

1. 2015 Symposium: Izzy Owen of Seton Hill University

2. 2015 Symposium: Sarah Belay and Sarah Modlin from the College of William and Mary

3. 2015 Symposium: Amanda Sciola and Kamil Wielechowski from Southern Connecticut State University

4. 2015 Symposium: Kaivalya Dandamundi and Shelby Edling of Virginia Commonwealth University

5. 2015 Symposium: Sophie Jurgensen from James Madison University

6. 2015 Symposium: Julia Gross from Brown University

7. 2015 Symposium: Erin Lockwood and Nijewel Holliday from Lincoln University

8. 2015 Symposium: Brigett Carvajal from Queensborough Community College

9. 2015 Symposium: Sara Lohbauer and Brittany Sisson from Florida Gulf Coast University

10. 2015 Symposium: Alexandra Crum and Trang Nguyen from the College of St. Scholastica

11. 2015 Symposium: Gina Brockman and Elise Lemanski from The Ohio State University

12. 2015 Symposium: Madeline Kosch and Kaylah Schuette from the University of Wisconsin, River Falls

13. 2015 Symposium: Cedric Penn Jr. from Morehouse College

14. 2015 Symposium: Alyssa Benjamin from Bucknell University

15. 2015 Symposium: Megan Ulbrich and Johnathan Schiebel from the University of Pittsburgh

16. 2015 Symposium: Kyle Cushman and Haley Fischman from Hope College

17. 2015 Symposium: Gillian Holder from the University of Louisiana, Monroe

18. 2015 Symposium: Buzz Hardin and Nolan Games from the Ouachita Baptist University

Assessment (2 videos) Go to channel page

Videos related to measuring the SEA-PHAGES program's impact on students.

Videos

1. An Introduction to SEA-PHAGES Assessment

2. Initial Findings from the PITS Survey

All Videos

Page 4 of 29

DNA Master: Review to Improve

This video shows how to check what changes the QC team made to your final annotation so that you can improve future annotations.

Added: Jun 17, 2020

Tags: DNA Master, Annotation, SEA-PHAGES, annotation, Bioinformatics

DNA Master: How to Annotate a -1 Translational Frameshift

Phage genomes often have an encoded translational frameshift that occurs at low frequency but is essential to produce complete virions. This video shows how to use DNA Master to call a frameshift where the ribosome slips -1 reading frame.

Added: Jun 17, 2020

Tags: DNA Master, Annotation, SEA-PHAGES, annotation, Bioinformatics

Using Aragorn to Find tRNA Genes in Phage Genomes

This video shows how to use Aragorn, a program that can scan phage genomes and identify and score potential tRNA genes.

Added: Jun 14, 2020

Tags: SEA-PHAGES, Bioinformatics, Aragorn

Page 4 of 29