Pathways Project: Annotation Videos
This series of videos is intended to help GEP students annotate a Pathways Project gene from start to finish.
Annotation Strategy
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 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.
Basic BLAST and Annotation Exercises
Dr. Hui-Min Chung (University of West Florida) has posted a series of 4 worksheets which can be used as a basic introduction to BLAST and annotation. These are very basic and suitable for use prior to the GEP annotation homework #1 and #2.
Introduction to the Complete GEP Gene Annotation Process
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.
Identify D. melanogaster Ortholog
This decision tree illustrates the list of criteria that can be used to determine the putative D. melanogaster ortholog of a predicted gene.
GEP Annotation Workflow
This workflow provides an overview of the key analysis steps and bioinformatics tools for the annotation of a predicted gene in the Drosophila F element GEP project.
TSS Annotation Workflow
This workflow provides an overview of the key steps and recommended search parameters for the annotation of transcription start sites.
Common Annotation Errors
This PowerPoint presentation describes the common errors observed in student annotations.
Annotation of Drosophila Primer
This PowerPoint presentation provides a brief primer on the recommended annotation strategy for Drosophila projects. The presentation provides an overview of the goals of the GEP annotation project, an introduction to RNA-Seq, web databases, and a discussion on the phases of the splice donor and acceptor sites.