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Annotation Strategy

Annotation Strategy Guide

This document illustrates how the strategies outlined in the Annotation Instruction Sheet can be applied to more challenging annotation cases.

Annotation Instruction Sheet

This document is a more in depth description of the evidence based annotation technique used by the GEP. This document is designed to complement and extend the basic technique described in the Annotation for D. virilis PowerPoint.

Annotation for D. virilis

This is a PowerPoint presentation describing the recommended strategies for annotating a D. virilis fosmid. The homology-based annotation strategy should also be applicable to annotation of D. erecta and D. mojavensis projects.

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.

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.

Annotating Splice Sites: Workflow

A one-page summary/flowchart of the logic process for identifying appropriate splice sites when annotating.

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.

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.