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 Form. An answer key (generic username and password required) is provided to assist instructors in checking the accuracy of the annotation and includes potential areas of confusion throughout.
The Annotation Form Exemplar is provided as an example of a completed Annotation Form ready for submission to the GEP’s Pathways Project. The optional questions were omitted from the exemplar.
This “Annotation Form” merged the “Annotation Report” and “Annotation Notebook” into a single document and the latter two items were archived.
The “Annotation Form” kept many of the Checks for Understanding type questions that were previously in the “Annotation Notebook.” However, given that not all faculty want their students to answer those questions, we marked any question that is NOT required for submission to the GEP as “OPTIONAL.” Currently the optional questions are organized as letters rather than numbers, which we hope will make it easy to quickly select and delete the OPTIONAL questions that faculty don’t wish to include. Again, all numbered questions are required for submission to the GEP for reconciliation.
Items that were previously asked for in the “Project Details” table of the “Annotation Report” are now available on the Genome Browser Gateway page for each species. Therefore, the “Project Details Table” instructions document is no longer needed.
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.
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.
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.
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.
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.
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.
This document describes the primary annotation goals to be included in the final oral presentation and written report for students enrolled in the Bio4342 course at WU.
