Annotation of Conserved Motifs in Drosophila

This walkthrough uses FlyBase, FlyFactorSurvey, and Patser to identify transcription factor binding sites in the region surrounding the transcription start site of onecut in D. biarmipes.

Annotation of a Drosophila Gene

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.