About This Page
To prepare to annotate genes, students are first introduced to the common tools available for annotation (BLAST, RepeatMasker, UCSC Genome Browser). This page contains a list of annotation tutorials developed by GEP faculty.
List of Annotation Tutorials and Walkthroughs
Generating Multiple Sequence Alignments with ClustalW
Dr. Susan Parrish (McDaniel College) developed a basic lecture and weblem exercise (found at the end of the lecture) on using ClustalW to generate multiple sequence alignments, phylograms, and cladograms. This lecture and exercise are given prior to beginning the GEP annotation projects. Students who submit their GEP annotation projects early are then asked to generate multiple sequence alignments and phylograms of the putative proteins encoded within their assigned contig or fosmid, compared to those related proteins encoded by other Drosophila species of interest to the GEP.
FlyBase for Undergrads
Dr. Hui-Min Chung (University of West Florida) and her students have developed an instructional video aimed at introducing undergraduate students to the research tools available at FlyBase.
- Last update: 02/12/2011
- Tags: FlyBase
Gene Annotation of Genomic DNA
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 and it also includes a sample GEP Annotation Report.