Drosophila F Element

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.

Annotation of Drosophila

This PowerPoint presentation describes the recommended annotation strategy for Drosophila projects. The presentation provides an overview of the goals of the GEP annotation project, an introduction to NCBI BLAST, web databases, and the issue of reading frames and phase.

GEP Digital Laboratory Notebook

Developed by Dr. Nick Reeves at Mt. San Jacinto College, Menifee Valley Campus, this PowerPoint presentation provides a brief overview of the Digital Lab Notebook, which provides detailed guidance to students on the GEP annotation strategy.

Motif Discovery in Drosophila

This walkthrough uses FlyBase RNA-Seq Search and the MEME suite to discover motifs that are enriched in a collection of D. melanogaster Muller F element genes that show similar expression patterns.

Annotation of Conserved Motifs in Drosophila

This walkthrough uses FlyBase, FlyFactorSurvey, and Patser to identify transcription factor binding sites in the region surrounding the transcription start site of onecut in D. biarmipes.