Lesson

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.

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.

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.