Genomic Annotation Lab Exercise
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.
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Gene Finding
Basic BLAST and Annotation Exercises
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.
Gene Annotation of Genomic DNA
Dr. James Bedard with students Amber Harlan and Joshua Machone presented a walkthrough on their annotation projects for a lunchtime talk series at Adams State College.
Introduction to the Complete GEP Gene Annotation Process
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.
Gene Finding in Chimpanzee
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.
Chimp Chunk Projects without Student Reports
Additional chimp chunk projects without student reports. Please contact Dr. Chris Shaffer for instructions on how to create additional chimp annotation projects.
Sample Chimp Chunk Reports
Three sample chimp chunk projects with student reports.
Analysis of a Chimp Chunk
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.
Guidelines for your Chimp Chunks Report
Brief guidelines with advice on annotating chimpanzee DNA, including what to put in the final report.
Chimp BAC Analysis: Genes and Pseudogene
A step-by-step tutorial that takes the student through a gene identification problem in a chimpanzee BAC sequence using predictions from a gene prediction program (Genscan), the UCSC Browser and BLAST.
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