Student Resources

Here's a step-by-step collection of videos that demonstrate how you can complete your GENI-ACT annotation assignments.

There's also a companion Training Manual by Dr. Stephen Koury that you can access here.  It will help you complete the GENI-ACT tasks.

Background and Getting Started

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.org 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.



Module 1:  Basic Information

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.


Module 2:  Sequence Based Similarity

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.


Module 3:  Structure Based Similarity

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.


Module 4:  Cellular Localization

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.


Module 5:  Alternative Open Reading Frames

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.

Module 6:  Enzymatic Function

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.

Module 7:  Duplication and Degradation

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.


Module 8:  Horizontal Gene Transfer

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.


Module 9:  RNA

Final Annotation

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.




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