Developed by Dr. Nick Reeves at Mt. San Jacinto College, Menifee Valley Campus, this PowerPoint presentation provides a brief overview of the Digital Lab Notebook, which provides detailed guidance to students on the GEP annotation strategy.
This worksheet will guide you through a series of basic steps that have been found to work well for annotation of species closely related to Drosophila melanogaster. It provides a technique that can also be the foundation of annotation in other, more divergent species but in those cases other special techniques will probably be needed.
This walkthrough uses the annotation of a gene on the D. biarmipes Muller F element to illustrate the GEP comparative annotation strategy. This document shows how you can investigate a feature in an annotation project using FlyBase, the Gene Record Finder, and the gene prediction and RNA-Seq evidence tracks on the GEP UCSC Genome Browser. The walkthrough then shows how you can identify the coordinates of each coding exon using NCBI BLAST, and also includes a discussion on the phases of the donor and acceptor splice sites. The walkthrough concludes by verifying the proposed gene model using the Gene Model Checker; it also includes a sample GEP Annotation Report.
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.
This PowerPoint presentation provides a brief introduction to the different types of RNA-Seq evidence tracks (e.g. Bowtie, TopHat, Cufflinks) that are on the GEP UCSC Genome Browser.
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.
