This document illustrates how students can apply the sequence improvement protocol described in the “Sequence Improvement Protocol for GEP Hybrid Assembly Projects” document to specific problems in a D. biarmipes sequence improvement project. Specifically, the walkthrough describes techniques for correcting consensus errors and for closing gaps.
A training document similar to “An Introduction to Consed,” this document contains a more detailed walkthrough that explores additional functions available in Consed.
A walkthrough that illustrates how students can use Consed to identify problematic regions in a genome assembly and strategies students can use to address these problems.
This document is a basic introduction to Consed, a program that allows users to visualize and manipulate a genome assembly. It provides screenshots of the various windows and points out the various functions available.
This is a series of three 3-hour exercises that guide students on the DNA Subway, an online workspace that integrates tools for genomic analysis in a student and educator-friendly environment. Exercise 1 was developed by Dr. Judy Brusslan (California State University, Long Beach). The Exercise I and II PowerPoints and Exercise II were developed by Dr. James Youngblom (California State University Stanislaus). The “Prospecting for Green Revolution Genes” presentation and Exercise III were developed by Dr. Nicholas Ewing (California State University, Sacramento) based on materials initially developed by members of the iPlant Collaborative.
This exercise was developed by Dr. Anya Goodman (California Polytechnic State University) and Dr. James Youngblom (California State University, Stanislaus). This exercise engages students in annotating genomic DNA from less famous species of Drosophila while teaching basic bioinformatics skills.
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.
Dr. Justin R. DiAngelo (Penn State Berks) has developed an exercise that takes students through a series of steps to annotate a gene in a Drosophila biarmipes contig. Students will construct a gene model using gene predictions, BLASTX searches, and the GEP UCSC Genome Browser mirror. Students will then verify their final gene model using the Gene Model Checker.
