Annotation checklist

Your instructor will assign you a login and a password that will allow you to work at this site, if you don't yet have this please contact your instructor.

Here is a quick checklist of what we will do for each gene in the database. Specific information on each of these tasks can be found by following the links in left menu bar.

1. Assign a function to the product of the gene.
2. Assign a name to the gene.
3. Assign or verify the start codon of the gene.
4. Select a category for the gene product.
5. Check the 'annotator' box when steps 1-4 are complete.

Note: If you don't feel comfortable doing any of these, or if you are having a particular problem with one, contact your instructor for assistance. Remember, this is a 'live' research project and we are relying on your accurate assessment of gene function!

Lets start by showing you how to get to the database that holds all the information on the genes. We have already identified all the genes for you, so what you need to do now is find information about what they are and what they do.

1. From the start page http://agro.vbi.vt.edu select the 'Annotation main page (beta version)' link
2. Select the 'Agrobacterium vitis (S4)' link
3. Select any replicon from the replicon overview list (e.g. chromosome 1). This may be assigned by your instructor or you may choose to work on your own.
4. Select 'click here' adjacent to the "protein coding genes" heading in the table.
5. You will see a table of all protein coding genes for the replicon you chose. We will only be working with the green highlighted genes at this point. Select the gene that was assigned by your instructor OR find one that says 'none' in the checked by column of the table. Click 'view/edit' to begin working on the gene.
6. Verify that the check boxes at the top that say 'annotator', 'supervisor' or 'guru' have NOT been checked. You cannot uncheck them if they have, just move to a different gene.
7. If this is your first time visiting the site you should look around the page to familiarize yourself with the different items. All information that you need to enter will be in the first box at the top of the page. The remaining boxes on the page are support sections to help you find information about the gene.
8. Begin annotation by following the links under the annotation heading in the left menu bar or just click the continue button below.
   

Note: I will use gene AVI0017 from S4 replicon I in the following examples.