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.
Developed by Dr. Ken Saville (Albion College) and Dr. Gerard McNeil (York College, City University of New York), this walkthrough provides a comprehensive overview of the entire GEP gene annotation process. This walkthrough includes a brief description of the research problem and step-by-step instructions on how to use the UCSC Genome Browser, FlyBase, the Gene Record Finder and NCBI BLAST to investigate a feature in a Drosophila erecta Muller F element annotation project. The walkthrough then shows how students can use the Gene Model Checker to verify a gene model; it also includes a sample GEP Annotation Report.
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.
Three sample chimp chunk projects with student reports.
Following the step-by-step tutorial “Chimp BAC Analysis: Genes and Pseudogene”, students should be ready to annotate a chunk of chimpanzee DNA themselves, presenting evidence to support their claim of a gene or pseudogene. An example student report from the Bio 4342 course at WU is available here.
Brief guidelines with advice on annotating chimpanzee DNA, including what to put in the final report.
