2011 Phagehunting Teacher Workshop
Genome for Annotation
Software and Computer Information
If you've been accepted to the workshop you should have received a software instructions and requirements document in the packet you received. Much of the same information can be found below.
Internet Access
You will need to follow these instructions that were included with your workshop materials, regardless of whether or not you will be bringing your own computer.
The two main bioinformatic tools we'll be using this year are DNAMaster and Phamerator.
DNAMaster
DNAMaster is an annotation genome editor developed and maintained by Dr. Jeffrey Lawrence at the University of Pittsburgh. During the workshop--and subsequently in your classrooms--this is the main tool you will use to locate and call genes in a phage genomic DNA sequence. As of now, this program only runs on Windows operating systems (though it can be installed within a virtual machine on a Mac). The program is available from Jeffrey Lawrence's Lab, but you should have received an installation disk with your workshop materials along with detailed instructions on how to install and update DNAMaster.
Phamerator
Phamerator is a tool, developed by Dr. Steve Cresawn at James Madison University, to compare phage gene products and genomes to one another and display the results of these comparisons in useful ways. It works by comparing all annotated mycobacteriophage gene products to one antoher, and then grouping genes with similar products into Phamilies, or "Phams." Here is a sample Pham. Phamerator runs in a Linux environment, so on a Mac or PC it must be installed within a virtual machine. To install, use the installation disk you received with your workshop materials and follow the instructions in the appropriate document.
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Annotation Guide
Our annotation guide is available online for download and use in your classrooms.