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Synteny

Synteny Introduction Slides

This resource is a slide deck offering an expanded introduction to synteny. Instructors are encouraged to use and modify to fit the needs of specific courses and students.

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

About Synteny Analysis

A one-page summary of the logic process used to determine if genes in a fosmid are syntenic with respect to D. melanogaster