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.
This series of videos is intended to help GEP students annotate a Pathways Project gene from start to finish.
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.
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.
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.
This decision tree illustrates the list of criteria that can be used to determine the putative D. melanogaster ortholog of a predicted gene.
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.
This workflow provides an overview of the key steps and recommended search parameters for the annotation of transcription start sites.
This PowerPoint presentation describes the common errors observed in student annotations.