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Annotation Strategy

Parasitoid Wasps Project: Annotation Walkthrough

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

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.

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.