Lecture

Fulton Lecture Notes

The lecture notes from a presentation by Bob Fulton point out some of the more advanced features of Consed, the base caller phred, and the assembler phrap. This document should be read after students have some experience using Consed but before they begin working on their fosmids.

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.

Overview of the Drosophila modENCODE Hybrid Assemblies

This PowerPoint presentation provides a general overview of the hybrid assemblies produced by the Baylor College of Medicine Human Genome Sequencing Center as part of the Drosophila modENCODE project. This presentation provides a brief introduction to the source of the raw sequence data and the protocol used by BCM-HGSC to construct the draft D. biarmipes genome assemblies.

Common Annotation Errors

This PowerPoint presentation describes the common errors observed in student annotations.

UNIX for Consed

This PowerPoint presentation discusses the basic directory structure required by Consed and the UNIX commands used to launch Consed.

Gene Finding in Chimpanzee

A step-by-step tutorial that takes the student through a gene identification problem in a chimpanzee BAC sequence using predictions from a gene finder (Genscan), the UCSC Browser and BLAST.

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.

Annotation of Drosophila

This PowerPoint presentation describes the recommended annotation strategy for Drosophila projects. The presentation provides an overview of the goals of the GEP annotation project, an introduction to NCBI BLAST, web databases, and the issue of reading frames and phase.