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.
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.
This decision tree illustrates the list of criteria that can be used to determine the putative D. melanogaster ortholog of a predicted gene.
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.
A one-page summary of the logic process used to determine if genes in a fosmid are syntenic with respect to D. melanogaster
This exercise allows students to learn how to use mRNA and Expressed Sequence Tags (ESTs) evidence to assist their annotation efforts. An answer key is available for instructors.
