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Parasitoid Wasps Project: Annotation Walkthrough

  • November 22, 2021November 29, 2021

This exercise will walkthrough an example of annotating a wasp venom gene for the Parasitoid Wasps Project. It will discuss wasp versions of common GEP annotation tools—Genome Browser, Gene Record Finder, and Gene Model Checker—and provide background for the interpretation of data tracks that are unique to the Parasitoid Wasps Project.

A Complex Drosophila Fosmid

  • August 15, 2020August 19, 2020

This fosmid from Drosophila virilis assembles into three contigs (a yellow clone). In this exercise, students must generate a final assembly by closing a gap, dealing with a mis-assembly, and improving low quality regions. Snapshots of the different stages of the assembly are stored as separate ace files.

A Simple Drosophila Fosmid

  • August 15, 2020August 19, 2020

This fosmid from Drosophila virilis assembles into a single contig (a green clone). In this exercise, students will need to identify regions in the assembly where additional data is needed and design additional sequencing reactions to bring the contig up to quality standards.

Identifying and Sorting Tandem Duplications and an Inverted Repeat

  • August 15, 2020August 19, 2020

Developed by the professional finishers at the WU Genome Institute (Holly Kotkiewicz and Jennifer Hodges), this walkthrough illustrates how you can use high quality discrepancies, Miniassembly, and cross_match to resolve a major misassembly in a D. ananassae project.

GEP Hybrid Assembly Walkthrough

  • August 15, 2020August 19, 2020

This document illustrates how students can apply the sequence improvement protocol described in the “Sequence Improvement Protocol for GEP Hybrid Assembly Projects” document to specific problems in a D. biarmipes sequence improvement project. Specifically, the walkthrough describes techniques for correcting consensus errors and for closing gaps.

Using Consed Graphically

  • August 15, 2020August 19, 2020

A training document similar to “An Introduction to Consed,” this document contains a more detailed walkthrough that explores additional functions available in Consed.

An Introduction to Consed

  • August 15, 2020August 19, 2020

A walkthrough that illustrates how students can use Consed to identify problematic regions in a genome assembly and strategies students can use to address these problems.

Introduction to the Complete GEP Gene Annotation Process

  • August 15, 2020August 19, 2020

Developed by Dr. Ken Saville (Albion College) and Dr. Gerard McNeil (York College, City University of New York), this walkthrough provides a comprehensive overview of the entire GEP gene annotation process. This walkthrough includes a brief description of the research problem and step-by-step instructions on how to use the UCSC Genome Browser, FlyBase, the Gene Record Finder and NCBI BLAST to investigate a feature in a Drosophila erecta Muller F element annotation project. The walkthrough then shows how students can use the Gene Model Checker to verify a gene model; it also includes a sample GEP Annotation Report.

Using FlyBase RNA-Seq Tools to Investigate Gene Expression Profiles

  • August 15, 2020January 2, 2022

This walkthrough illustrates how GBrowse and the RNA-Seq tools at FlyBase can be used to identify genes with similar expression patterns. This walkthrough provides an introduction to the TopoView RNA-Seq track in FlyBase GBrowse, the FlyBase Expression Profile Search tool, and the Expression Similarity Search tool. It also illustrates how the Gene2Function web site can be used to infer the function of a D. melanogaster gene based on the functions of its orthologs in other model organisms.