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Home » Annotation Strategy

Annotation Strategy

Pathways Project Primer

This PowerPoint presentation provides a primer on the recommended annotation strategy for the Pathways Project. The presentation provides an overview of the goals of the Pathways Project annotations, an introduction to RNA-Seq, web databases, and a discussion on the phases of the splice donor and acceptor sites.

Genomic Neighborhood Check For Understanding

This was created in response to a member mentioning their students really struggled with the genomic neighborhood and the member didn’t realize until they were already too far into the annotation to correct their misconceptions. This is meant to be a quick in-class and/or homework assignment.

Pathways Project: Annotation Videos

The Pathways Project is focused on annotating genes found in well-characterized signaling and metabolic pathways across the Drosophila genus. The current focus is on the insulin signaling pathway which is well-conserved across animals and critical to growth and metabolic homeostasis. The long-term goal of the Pathways Project is to analyze how the regulatory regions of genes evolve in the context of their positions within a network. For a general project overview, see the following video by Dr. Laura K. Reed:

Pathways Project Walkthrough Series

This series of videos based on the Pathways Project Annotation Walkthrough is intended to help GEP students annotate a Pathways Project gene from start to finish. The full series is available on the GEP YouTube Channel.

Pathways Gene Annotation Walkthrough Videos

Introduction

Part 1: Examine genomic neighborhood surrounding target gene in D. melanogaster

Part 2.1: Retrieve protein sequence of target gene in D. melanogaster

Part 2.2: Perform a BLAST search of D. melanogaster protein against the target species' genome

Part 2.3: Summarize tblastn results for protein on target species' scaffold

Part 3.1: Examine evidence for a protein-coding gene in region surrounding the tblastn alignment in the target species

Part 3.2: Use synteny to gather additional evidence for the ortholog assignment

Part 4: Determine target gene’s structure in D. melanogaster

Part 5: Determine approximate location of coding exons (CDS's) in target species

Part 6.1: Verify start codon coordinates

Part 6.2: Verify stop codon coordinates

Part 6.3: Determine phases of donor and acceptor splice sites

Part 6.4: Use spliced RNA-Seq reads to verify coordinates for Intron-1

Part 6.5: Use splice junction predictions to verify coordinates for second intron

Part 7.1: Verify gene model of protein

Part 7.2: Download files required for project submission

Part 7.3: Merge project files

Appendix A: Combining (or Batching) BLAST Searches

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.

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 Other Genomic Features within the F Element Project

This presentation illustrates the unusual genomic features that GEP students have encountered as part of their annotation of Muller F Elements from Drosophila ananassae and D. bipectinata. The Muller F Elements in these two species have undergone substantial expansion compared to D. melanogaster. The presentation describes the basic strategy for identifying pseudogenes, retrogenes, partial gene duplications, pseudogene clusters, and nuclear mitochondrial DNA segments (NUMT) within these F Element annotation projects.