Pathways Project: Annotation Videos
This series of videos is intended to help GEP students annotate a Pathways Project gene from start to finish.
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BLAST
Pathways Project: Annotation Walkthrough
The Pathways Project is focused on annotating genes found in well characterized signaling and metabolic pathways across the Drosophila genus. This walkthrough illustrates how to apply the GEP annotation strategy for the Pathways Project to construct a gene model for the Ras homolog enriched in brain (Rheb) gene in Drosophila yakuba.
Annotation Unix Worksheet
Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.
Command Line Unix: BLAST, RepeatMasker, Herne
PowerPoint presentation with instructions for running BLAST, RepeatMasker, and the BLAST output viewer Herne on the command-line.
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.
Genomic Annotation Lab Exercise
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.