C4

Pathways Project: Annotation Workflow

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.

Pathways Project: Annotation Notebook

The Pathways Annotation Notebook will help GEP students keep track of their work as they are annotating, and then they can use the notebook to fill out the report form. This notebook does not have to be submitted to GEP, it’s just an extra resource students might find helpful.

Pathways Project: Annotation Report

GEP students will use the Report Form document to submit their annotation results for the Pathways Project. The Project Details Table handout will show students how to fill out the first page of the Annotation Report. The Report Form Exemplar is provided as an example of a completed report. The Annotation Workflow is a one page summary of the annotation protocol.  

Gene Annotation using GEP Tools

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.

The Human Genome and Personalized Medicine

Developed by Dr. Anya Goodman (California Polytechnic State University) and Dr. James Youngblom (California State University Stanislaus), this computer laboratory is designed to introduce students to the analysis of DNA sequences and to the effects of bioinformatics on access to health information by scientists, doctors, and the general public.

Plant Genes Annotation and Analysis

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

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

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.