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.
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F Element Project: Annotation Report
This document is the revised annotation report that GEP students will use to report their annotation results to the GEP.
Drosophila willistoni Annotation Report
F Element Expansion Annotation Reports
Simple Annotation Problem
This worksheet will guide you through a series of basic steps that have been found to work well for annotation of species closely related to Drosophila melanogaster. It provides a technique that can also be the foundation of annotation in other, more divergent species but in those cases other special techniques will probably be needed.
Annotation of a Drosophila Gene
This walkthrough uses the annotation of a gene on the D. biarmipes Muller F element to illustrate the GEP comparative annotation strategy. This document shows how you can investigate a feature in an annotation project using FlyBase, the Gene Record Finder, and the gene prediction and RNA-Seq evidence tracks on the GEP UCSC Genome Browser. The walkthrough then shows how you can identify the coordinates of each coding exon using NCBI BLAST, and also includes a discussion on the phases of the donor and acceptor splice sites. The walkthrough concludes by verifying the proposed gene model using the Gene Model Checker; it also includes a sample GEP Annotation Report.
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.
Browser-Based Annotation and RNA-Seq Data
This exercise continues your introduction to practical issues in comparative annotation. You will be annotating genomic sequence from the dot chromosome of Drosophila mojavensis using your knowledge of BLAST and some improved visualization tools. You will also consider how best to integrate information from high-throughput sequencing of expressed RNA.
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.
Common Finishing Errors
This PowerPoint presentation describes the common errors observed in student finishing projects.
A Complex Drosophila Fosmid
This fosmid from Drosophila virilis assembles into three contigs (a yellow clone). In this exercise, students must generate a final assembly by closing a gap, dealing with a mis-assembly, and improving low quality regions. Snapshots of the different stages of the assembly are stored as separate ace files.
A Simple Drosophila Fosmid
This fosmid from Drosophila virilis assembles into a single contig (a green clone). In this exercise, students will need to identify regions in the assembly where additional data is needed and design additional sequencing reactions to bring the contig up to quality standards.