Skip to content
Search
Close this search box.
Genomics Education Partnership logo
Contact Us
Genomics Education Partnership logo
Contact Us
Home » Wilson Leung » Page 2

Wilson Leung

Annotation of a Drosophila Gene

This walkthrough uses the annotation of a gene on the D. biarmipes Muller F element to illustrate the GEP comparative annotation strategy. This document shows how you can investigate a feature in an annotation project using FlyBase, the Gene Record Finder, and the gene prediction and RNA-Seq evidence tracks on the GEP UCSC Genome Browser. The walkthrough then shows how you can identify the coordinates of each coding exon using NCBI BLAST, and also includes a discussion on the phases of the donor and acceptor splice sites. The walkthrough concludes by verifying the proposed gene model using the Gene Model Checker; it also includes a sample GEP Annotation Report.

Annotation of Drosophila Primer

This PowerPoint presentation provides a brief primer on the recommended annotation strategy for Drosophila projects. The presentation provides an overview of the goals of the GEP annotation project, an introduction to RNA-Seq, web databases, and a discussion on the phases of the splice donor and acceptor sites.

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.

A Complex Drosophila Fosmid

This fosmid from Drosophila virilis assembles into three contigs (a yellow clone). In this exercise, students must generate a final assembly by closing a gap, dealing with a mis-assembly, and improving low quality regions. Snapshots of the different stages of the assembly are stored as separate ace files.

A Simple Drosophila Fosmid

This fosmid from Drosophila virilis assembles into a single contig (a green clone). In this exercise, students will need to identify regions in the assembly where additional data is needed and design additional sequencing reactions to bring the contig up to quality standards.

The D. grimshawi dot chromosome

This PowerPoint presentation explains our strategy, detailing the source of the raw sequence data for the D. grimshawi dot chromosome.

Workflow to Resolve Misassembly

A flowchart that illustrates the key decisions and strategies when dealing with misassemblies that are caused by collapsed repeats.

Common Misassembly Protocols

This document describes a list of protocols that are frequently used to resolve misassembly.

GEP Misassembly Tools User Guide

This document describes the list of tools developed by the GEP to facilitate incorporation of additional reads from the NCBI Trace Archive into a sequence improvement project. This document shows how to install the tools, and illustrates their use in two case studies (walkthroughs) of challenging fosmid assemblies.

Identifying and Sorting Tandem Duplications and an Inverted Repeat

Developed by the professional finishers at the WU Genome Institute (Holly Kotkiewicz and Jennifer Hodges), this walkthrough illustrates how you can use high quality discrepancies, Miniassembly, and cross_match to resolve a major misassembly in a D. ananassae project.