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Parasitoid Wasps Project: Annotation Workbook

November 22, 2021December 1, 2021

For the Parasitoid Wasps Project gene annotation, project submission will consist of a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein. This Annotation Workbook is an Excel file with space to fill out all the necessary information for the gene annotation.

If it is done correctly, filling out the workbook will also auto-populate a GFF file that can be used for testing the accuracy of gene models (described in the “Checking Accuracy of the Gene Model (Alternative to Gene Model Checker)” section of the “Annotation Workbook Directions“). Please note that everything should be filled out exactly as described: the vocabulary and formatting need to be very precise to make a functional GFF file.

The “Example” sheet has been completed for you to reference while completing the “Transcript” sheet.

Parasitoid Wasps Project: Annotation Workbook Directions

November 22, 2021December 1, 2021

This document provides directions for how to complete and obtain the items needed to submit a Parasitoid Wasps Project annotation—a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein.

Parasitoid Wasps Project: Annotation Walkthrough

November 22, 2021November 29, 2021

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 Videos

January 19, 2021March 8, 2021

This series of videos is intended to help GEP students annotate a Pathways Project gene from start to finish.

Pathways Project: Annotation Workflow

November 13, 2020August 11, 2021

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.

Pathways Project: Annotation Report Exemplar

September 14, 2020March 11, 2022

GEP students use the Annotation Report form to submit their annotation results for the Pathways Project. The Annotation Report Exemplar is provided as an example of a completed report.

Pathways Project: Annotation Report

September 14, 2020March 11, 2022

GEP students will use the Report Form document to submit their annotation results for the Pathways Project. The Project Details Table handout will show students how to fill out the first page of the Annotation Report. The Report Form Exemplar is provided as an example of a completed report.

Pathways Project: Annotation Notebook D. pseudoobscura Homework Key

September 14, 2020June 3, 2022

Students can apply what they learned in the Pathways Project: Annotation Walkthrough to construct a gene model for Rheb in D. pseudoobscura by completing the Pathways Project: Annotation Notebook. An answer key is provided to assist in checking the accuracy of the annotation and includes potential areas of confusion throughout.

Pathways Project: Annotation Notebook

September 14, 2020August 31, 2021

The Pathways Annotation Notebook will help GEP students keep track of their work as they are annotating, and then they can use the notebook to fill out the report form. This notebook does not have to be submitted to GEP, it’s just an extra resource students might find helpful.

Pathways Project: Annotation Walkthrough

August 15, 2020January 10, 2022

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.