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Student and Faculty Tools for Generating High-Quality Phage Annotations

By Kristen Butela1, Hui-Min Chung2, Lee Hughes3, Denise L Monti4

1. University of Pittsburgh 2. University of West Florida 3. University of North Texas 4. University of Alabama at Birmingham

Phage genome annotation requires collaboration between faculty and their student research team. This set of resources provides tools to assist both students and faculty in the evaluation and submission of a complete phage genome.

Listed in Teaching Materials | resource by group HHMI Science Education Alliance (SEA) Faculty Group

Version 1.0 - published on 07 Aug 2020 doi:10.25334/WDMM-SV47 - cite this

Licensed under CC Attribution-ShareAlike 4.0 International according to these terms

Checking Annotations.jpg


The ever-decreasing cost of full genome sequencing and the development and widespread availability of genome annotation programs have increased genome annotation accessibility.  Auto-annotation programs, such as Glimmer and GeneMark, are often used for gene prediction, but manual curation of genomes can improve gene calling and detect nuances in the genome.  Phage genomes are particularly suited for manual curation because the genomes tend to be small (<250kbp).  In the HHMI SEA-PHAGES courses, manual curation of phage genomes provides students an opportunity to participate in authentic research while learning genetics, bioinformatics, proteomics, and data science. This set of resources provides tools for students and faculty to use to ensure the highest quality phage genome annotation is submitted at the conclusion of the term.  


Learning Objectives

After completing this module, students should be able to:

  1. Use a suite of bioinformatics programs to determine whether an ORF should be called a gene

  2. Analyze data from a suite of bioinformatics programs to make a determination of the most likely start codon for a gene

  3. Explain why the start codon selected for a gene is the most likely start codon

  4. Find and annotate tRNAs in phage genomes

  5. Use a suite of bioinformatics programs to assign a putative function to a called gene

  6. Explain why an assigned function is appropriate for a particular putative gene. 

  7. Evaluate various elements of a typical annotated phage genome to identify inconsistencies and potential areas of improvement (putative gene calls, frameshifts, large gaps, membrane proteins, putative function assignments)


After completing this module, faculty should be able to:

  1. Actively involve students in the genome quality control/peer reviewing process.

  2. Use the DNA Master Frames window, the genome comparison tool in DNA Master, and/or Starterator to quickly identify putative gene calls and/or significant gaps that warrant further review.

  3. Quickly evaluate called functions for all putative genes in a phage genome. 

  4. Create correctly formatted complete notes and minimal DNA Master files when using PECAAN as a supplementary annotation tool.


How is the module structured to promote student development as a scientist? 

Phage genome annotation work has many opportunities for supporting students as developing scientists.  By using the resources provided in this set, students have a set of tools that empowers them to complete a challenging project while working collaboratively with their peers.  By nature of the work, students will face ambiguity while analyzing data from multiple bioinformatics projects but the tools provided, along with instructor mentorship, will provide a format for them to work through the ambiguous data to make the best gene start decisions possible.  


Intended Teaching Setting

Course level:  undergraduate students, SEA-PHAGES students.

Instructional Setting:  in-person classroom, online

Implementation Time Frame:  varies depending on genome size


Learning activity document(s)

  • Faculty Guide - Resources for Submission of Quality Phage Genome Annotations

  • Student Genome Annotation Worksheet 

  • Student tRNA Annotation Worksheet

  • Genome Annotation Summary Spreadsheet

  • Student Group Quality Control Checklist

  • Whole-genome Starterator Output File Instructions


Assessment document(s)



Cite this work

Researchers should cite this work as follows:


HHMI Science Education Alliance (SEA) Faculty Group

HHMI Science Education Alliance (SEA) Faculty Group group image

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