Advanced Student

Annotation Unix Worksheet

Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.

Introduction to UNIX Exercise

A simple exercise on using simple Unix commands to navigate to different directories and manipulate files.

Using FlyBase RNA-Seq Tools to Investigate Gene Expression Profiles

This walkthrough illustrates how GBrowse and the RNA-Seq tools at FlyBase can be used to identify genes with similar expression patterns. This walkthrough provides an introduction to the TopoView RNA-Seq track in FlyBase GBrowse, the FlyBase Expression Profile Search tool, and the Expression Similarity Search tool. It also illustrates how the Gene2Function web site can be used to infer the function of a D. melanogaster gene based on the functions of its orthologs in other model organisms.

RNA Quantitation from RNA-Seq Data

Developed by Dr. Jeremy Buhler, this PowerPoint presentation provides an overview of the approaches for quantifying transcript abundance based on RNA-Seq data. The presentation includes a discussion on the benefits and limitations of the two approaches commonly used for RNA quantitation – RPKM and TPM.

Motif Discovery in Drosophila

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.

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.

Behavior and Limitations of Motif Finding

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.