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Chinmay Rele

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

Pathways Project: Annotation Form

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.

Annotation Form
Annotation Form
Annotation Form Exemplar
Annotation Form Exemplar
Annotation Form
D. pseudoobscura Key
Annotation Form
D. pseudoobscura Key

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.