To finish things up are these two topics. Module 9 explores the RNA that your gene makes, and there's a very short finale regarding to annotations. The guide for this is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
Genes aren't as fixed as you might think. It's possible that an organism can pick up genes from a completely species. You can test if the gene you're working on might have some interesting ancestral connections. The guide for this is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
Evolution is driven by changes in genes. Sometimes genes are inadvertently duplicated during replication. This provides an "extra copy" that is free to vary through mutation, sometimes providing extended function. A good example is the family of hemoglobin genes in mammals. Members of a family which arose through duplication can also mutate and lose function. This module lets you explore these scenarios. The guide for this is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
Not all proteins are enzymes - but many are! You can use databases of biochemical pathways (such as KEGG) to look for a particular enzyme that may or not be in the genome of the organism you're studying. The guide for this is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
There's a great guide regarding how to ensure that the automated gene annotator that identified the gene you're working on chose the proper start location for translation. The guide is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
There's a great guide regarding how to determine where the protein from your gene is likely to appear in the cell. This guide is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
There's a great guide regarding how the predicted amino acid sequence sets up the structure of the polypeptide. Well-studied genes with similar structure might have good clues as to what the gene your working on does. This guide is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
There's a great guide regarding how to use the nucleotide sequence of your gene to compare it with other well-studied genes in databases. Similar sequences can give good insight into what your gene does. The guide is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
There's a great guide regarding Basic Information about your geneIt is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
In the student tab there are resources to help students use the GENI-ACT resources.
As an instructor, you might choose to alter these to fit your plans. They are in DropBox, a free cloud storage platform. If you wish to create your own DropBox account, click here. This account is not necessary to view these files.
IMG/EDU holds great first-pass annotations of genes with predictions that students can test using the GENI-ACT software. Dr. Scott ran through how to choose a genome using IMG in the "Interlude" section of this blog.
This movie shows how you can do a "Gene Search" in IMG to find a gene of interest (you could do an exercise with your students in advance to find out what they're interested in). You paste the Locus_ID into GENI-ACT and create an assignment based on this (Or these! You can do more than one!)
You can pick a gene right from GENI-ACT. Perhaps you could ask your students to do some research and write down what gene or genes they might like to work with. You can use your browser's "Find" function to look for similar names.
Step 3: After students have created accounts, create an assignment!
Have your students create their own accounts.
Ensure you provide them with your class token so that they appear in
your roster. Once they've done so, you can "form a team" to which the
assignment will be linked. Here's the part that can be confusing:
GENI-ACT is designed to allow a single student to annotate a bunch of
genes, and annotations can be done individually or through teams. And
the teams can be changed from assignment to assignment.
One way to remember this is TAGM (tag'em). This stands for the steps:
Team creation - assignments are linked to teams; students are put into teams.
Assignment creation - Name your assignment and add a description.
Gene List (This will be covered in the next three videos to show different ways to pick your genes).
Merge - Apply the gene(s) in your assignment to student teams.
Note that separate videos will detail how to create your gene list.
In order to participate in your instructor's GENI-ACT assignment, you'll need to make an account. By doing so, you'll be in the instructor's roster and he or she can create assignments for you to complete.
Before you create your account, be sure to get your Class Token. This will be provided by your instructor through an email or posted on your class Learning Management System (Moodle, BlackBoard, or other website).
Go to http://geni-act.com and set up your account. The video below walks you through the process (although you can probably figure it out for yourself!). There's also a great guide regarding Background Information about gene annotation and GENI, and Getting Started with GENI. It is in Dropbox (you don't need an account in Dropbox to get these, but it's handy free cloud storage.) The guide can be downloaded here.
After your account is established - you'll get an email letting you know you're approved - you need to create a class. This will create a "virtual space" or "classroom" that is identified by a Course Token (also called a Class ID on some GENI-ACT screens).
Students will use the Token when they create their account. This puts them into that "virtual space" (class). They will then appear in your Roster. You need them in there before you can create assignments for them.
If you're an instructor, you will want to register as such with the GENI-ACT administrators. Please email GoodnerBW@hiram.edu in order to get your account set up.
The
Microbial Genome Annotation Network (MGAN)provides authentic and inexpensive research opportunities in microbial genome analysis (Figure 1). It is geared toward high school
and undergraduate students.
Figure 1. The History of GENI-ACT - websites that informed the GENI-ACT model and practice.
MGAN acts in collaboration with several groups and curators:
the Genomics Education National Initiative (GENI)
project,
Dr. Cheryl Kerfeld (University of California, Berkley, CA)
Dr.
Brad Goodner (Hiram College, OH)
the Openmods system of Dr. Roy Welch (Syracuse University, NY),and
the National Science Foundation
The available technology includes:
an
online toolkit that consolidates publicly available bioinformatics tools into
a single platform (click here for a list), and
online collaboration tools and wet-lab resources (e.g.,
bacterial strains, primers and plasmids) for functional genomics studies.
The toolkit is called GENI-ACT (Genomics Education National
Initiative - Annotation Collaboration Toolkit). GENI-ACT represents
an updated and
independent version of the Department of Energy Joint Genome Institute's
IMG-ACT platform, with new features added by collaboration
with the GENI collaboration platform. To
date, more than 100 undergraduate and high school instructors are using
GENI-ACT in their classrooms and personal research since it went live in
2014. This blog provides educational resources for those trained in using GENI-ACT.
