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.
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Annotation of Transcription Start Sites in Drosophila
This walkthrough illustrates the GEP protocol for the comparative annotation of transcription start sites (TSS) in D. biarmipes. The walkthrough also includes a sample GEP TSS Report for the TSS annotation of onecut.
Detecting and Interpreting Genetic Homology: Lecture Notes on Alignment
Notes from a lecture on sequence alignment given by Dr. Jeremy Buhler in the Bio 4342 course at WU. The lecture covers the theory behind BLAST as well as some of the potential problems and limitations of BLAST.
Reconcile Sequence Improvement Projects
All GEP projects are completed at least twice independently by GEP students. This document describes how to check two or more submissions of a finishing project for congruence. Ordinarily this is done centrally at Washington University, but in some cases may be of interest at a given school.
Restriction Digests: A Tool to Check Your Findings
One of the main tools used to verify the correctness of a genome assembly is comparison of an in-silico restriction digest to the real restriction digest data generated by the WU Genome Center. This document also covers how students can use the restriction digest data early in the assembly process to determine the number of copies of repeats in a given cluster or to estimate gap sizes.
Sequence Improvement Protocol for GEP Hybrid Assembly Projects
This document describes the GEP protocol for improving the hybrid assemblies produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC). This document is designed to work in concert with the “GEP Hybrid Assembly Walkthrough” that illustrates how students can apply this protocol to specific issues that they might encounter during the sequence improvement process.
TSS Module Primer: Review of Transcription, Promoter Structure, and Chromatin Packaging
This primer includes some biological concepts that may be helpful to review prior to working with the four TSS Modules, including: a brief review of gene transcription, mRNA processing, promoter structure, and chromatin.
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
Chimp BAC Analysis: Genes and Pseudogene
A step-by-step tutorial that takes the student through a gene identification problem in a chimpanzee BAC sequence using predictions from a gene prediction program (Genscan), the UCSC Browser and BLAST.