Annotation Unix Worksheet
Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.
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Introduction to UNIX Exercise
A simple exercise on using simple Unix commands to navigate to different directories and manipulate files.
Unix Commands: Quick Reference Sheet
A Unix reference sheet for commonly used Unix commands.
Command Line Unix: BLAST, RepeatMasker, Herne
PowerPoint presentation with instructions for running BLAST, RepeatMasker, and the BLAST output viewer Herne on the command-line.
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.
RNA-Seq: a Closer Look at Read Mapping
Developed by Jeremy Buhler, this PowerPoint presentation provides an introduction to the core algorithms that form the basis for efficient mapping of RNA-Seq reads against a genome or transcriptome. The video that accompanies this presentation was developed by Leocadia Paliulis (Bucknell University).
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.