The Annotation Workflow is a one page summary of the annotation protocol for the Pathways Project. This workflow provides an overview of the key analysis steps and bioinformatics tools for the annotation of a putative ortholog.
GEP students use the Annotation Report form to submit their annotation results for the Pathways Project. The Annotation Report Exemplar is provided as an example of a completed report.
GEP students will use the Report Form document to submit their annotation results for the Pathways Project. The Project Details Table handout will show students how to fill out the first page of the Annotation Report. The Report Form Exemplar is provided as an example of a completed report.
Students can apply what they learned in the Pathways Project: Annotation Walkthrough to construct a gene model for Rheb in D. pseudoobscura by completing the Pathways Project: Annotation Notebook. An answer key is provided to assist in checking the accuracy of the annotation and includes potential areas of confusion throughout.
The Pathways Annotation Notebook will help GEP students keep track of their work as they are annotating, and then they can use the notebook to fill out the report form. This notebook does not have to be submitted to GEP, it’s just an extra resource students might find helpful.
This walkthrough uses FlyBase RNA-Seq Search and the MEME suite to discover motifs that are enriched in a collection of D. melanogaster Muller F element genes that show similar expression patterns.
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.
Developed by Dr. Jeremy Buhler, this exercise uses MEME to discover putative regulatory motifs in a collection of D. melanogaster promoter sequences. It also illustrates some of the challenges associated with motif finding and the limitations of motif finding programs.
This document contains the notes from a lecture on motif finding given by Dr. Jeremy Buhler in the Bio 4342 course at WU. The lecture covers the different approaches used to represent sequence motifs and to search for sequence motifs in a genome.
This workflow provides an overview of the key steps and recommended search parameters for the annotation of transcription start sites.
