Skip to content
Home » Gene Finding

Gene Finding

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.

Pathways Project: Annotation Workflow

  • November 13, 2020August 11, 2021

The Annotation Workflow is a one page summary of the annotation protocol for the Pathways Project. This workflow provides an overview of the key analysis steps and bioinformatics tools for the annotation of a putative ortholog.

Gene Annotation using GEP Tools

  • August 15, 2020August 19, 2020
Dr. Julie Emerson (Amherst College) has developed a simple introduction to the GEP annotation project for the 2012 ABLE conference. This set of documents provides an overview of the GEP’s scientific and educational goals and then goes through examples of how GEP materials are being utilized at multiple colleges and universities, focusing on gene annotation in an introductory biology course at Amherst College.

Plant Genes Annotation and Analysis

  • August 15, 2020August 19, 2020

This is a series of three 3-hour exercises that guide students on the DNA Subway, an online workspace that integrates tools for genomic analysis in a student and educator-friendly environment. Exercise 1 was developed by Dr. Judy Brusslan (California State University, Long Beach). The Exercise I and II PowerPoints and Exercise II were developed by Dr. James Youngblom (California State University Stanislaus). The “Prospecting for Green Revolution Genes” presentation and Exercise III were developed by Dr. Nicholas Ewing (California State University, Sacramento) based on materials initially developed by members of the iPlant Collaborative.

Finding Genes in a New Fly Genome

  • August 15, 2020August 19, 2020

This exercise was developed by Dr. Anya Goodman (California Polytechnic State University) and Dr. James Youngblom (California State University, Stanislaus). This exercise engages students in annotating genomic DNA from less famous species of Drosophila while teaching basic bioinformatics skills.

A Simple Annotation Exercise

  • August 15, 2020August 19, 2020

Dr. Justin R. DiAngelo (Penn State Berks) has developed an exercise that takes students through a series of steps to annotate a gene in a Drosophila biarmipes contig. Students will construct a gene model using gene predictions, BLASTX searches, and the GEP UCSC Genome Browser mirror. Students will then verify their final gene model using the Gene Model Checker.

Genomic Annotation Lab Exercise

  • August 15, 2020August 19, 2020

Dr. Marian Kaehler (Luther College), in collaboration with Jacob Jibb, has written an annotation lab. This lab will ask students to annotate a gene from the D. erecta genome.