This series of modules introduces students to the statistical platform R using an integrated development environment of RStudio. Both softwares can be downloaded for free. Once downloaded and installed according to Module 0, students should watch the accompanying video for an introduction to the new environment. Module 1 presents an exercise where students work with genomic sequence alignment data to learn how to construct R commands while performing basic summary statistics and making basic plots.
This was created in response to a member mentioning their students really struggled with the genomic neighborhood and the member didn’t realize until they were already too far into the annotation to correct their misconceptions. This is meant to be a quick in-class and/or homework assignment.
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 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 exercise continues your introduction to practical issues in comparative annotation. You will be annotating genomic sequence from the dot chromosome of Drosophila mojavensis using your knowledge of BLAST and some improved visualization tools. You will also consider how best to integrate information from high-throughput sequencing of expressed RNA.
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.
Exercise that uses UNIX tools (command-line BLAST and RepeatMasker) for gene annotations.
A simple exercise on using simple Unix commands to navigate to different directories and manipulate files.
Students can practice using Consed by working on a mouse contig. This exercise poses various challenges that students may encounter when working on their own projects.
