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.
Dr. Justin R. DiAngelo (Penn State Berks) and Dr. Alexis Nagengast (Widener University) have developed an exercise that introduces students to the basic functionality of the NCBI web site and NCBI BLAST. Students will use NCBI BLAST to identify the putative orthologs of the human Leptin gene in other species.
The Pathways Project is focused on annotating genes found in well characterized signaling and metabolic pathways across the Drosophila genus. This walkthrough illustrates how to apply the GEP annotation strategy for the Pathways Project to construct a gene model for the Ras homolog enriched in brain (Rheb) gene in Drosophila yakuba.
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.
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.
Dr. Marian Kaehler (Luther College), in collaboration with Jacob Jibb, has written an annotation lab. This lab will ask students to annotate a gene from the D. erecta genome.
