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.
Similar to the Lecture Notes on Alignment, this is a PowerPoint presentation given by Dr. Jeremy Buhler for the GEP faculty and TA workshops. This presentation covers the basics of alignment, essential for students to correctly interpret BLAST results.
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.
Developed by Jeremy Buhler, this PowerPoint presentation provides an introduction to the core algorithms that form the basis for efficient mapping of RNA-Seq reads against a genome or transcriptome. The video that accompanies this presentation was developed by Leocadia Paliulis (Bucknell University).
PowerPoint presentation with instructions for running BLAST, RepeatMasker, and the BLAST output viewer Herne on the command-line.
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.
This PowerPoint presentation explains our strategy, detailing the source of the raw sequence data for the D. grimshawi dot chromosome.
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.
This lecture by Dr. Sarah Elgin (Washington University in St. Louis) provides a general overview of the Genomics Education Partnership. It describes the current GEP research problem of identifying factors involved in heterochromatin formation and maintenance through comparative genomics in Drosophila.
This PowerPoint presentation provides a brief introduction to the different types of RNA-Seq evidence tracks (e.g. Bowtie, TopHat, Cufflinks) that are on the GEP UCSC Genome Browser.
