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.
This 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.
Dr. Hui-Min Chung (University of West Florida) has posted a series of 4 worksheets which can be used as a basic introduction to BLAST and annotation. These are very basic and suitable for use prior to the GEP annotation homework #1 and #2.
This lab is an updated, stand-alone version of the bioinformatics exercise originally developed for Bio 3055 at Washington University. This exercise introduce students to the genetic basis of disease using the KRas protein.
This exercise continues your introduction to practical issues in comparative annotation. You will be annotating genomic sequence from the dot chromosome of Drosophila mojavensis using your knowledge of BLAST and some improved visualization tools. You will also consider how best to integrate information from high-throughput sequencing of expressed RNA.