Defining a product

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

1. Scan the blast results to select a tentative product ID for the gene.

• You can see these in the Blast area of the page (about 4 boxes from the top). Note in this case that all the top hits are to hypothetical or conserved hypothetical proteins. Here is the difference:

• Now, take a look at the products/functions of the top 10 or so hits in the blast. If there is a consistency among the names then that is likely the function. In our example they are all hypothetical or conserved hypothetical genes. Other genes may be a bit more diverse, for example 6 of 10 hits may be to ABC transporters so you would select that product. All other products use the same criteria as in selecting conserved hypothetical genes (i.e. a match at or below 10-3 and 75% coverage).
  
• This gene would be tentatively assigned the product name: Conserved hypothetical protein.
  
• NOTE: All gene products are followed by the word 'protein': hypothetical protein, ABC transporter, membrane spanning protein.

2. Assignments should be confirmed based on further analysis of the domains found in the protein:

• Domains: evolutionarily conserved protein segments that retain a similar function.
  
• The next thing to confirm for a product is whether or not domains are present that support our choice of product. Domain information can be viewed in the 'other information' window under interpro results. This will be modified shortly to show domains visually. Take a look at the domains. Do they support the product? For our example there are NO domains for gene AVI0017, which supports our annotation as conserved hypothetical (since these proteins have no known function). If we had an ABC transporter we would expect to see domains supporting that product ID. For example 'binding protein dependent transport system inner membrane component' for ABC transporter membrane spanning proteins. Follow the links to interpro to learn about the function of the domain, this will help you decide if it supports your selected product choice.

private comments: Whenever you change anything in the database you should keep notes in the window at the bottom of the annotation page in the field 'private comments'. You can use this area to justify any changes that you have made. This will clarify your reasoning both for your instructor, as well as any member of the research team that views your data. In our example you might note that the top 6-7 blastp hits were to hypothetical or conserved hypothetical, AND that no domains were present so you chose Conserved hypothetical. This is mostly for your benefit so you can review what they did and why. I will see if we can change this so annotators will be asked directly to justify choices prior to changes being accepted.

3. When you are sure that you have the right product enter it in the product field at the top of the page. All you need to do now is hit the 'update' button located at the top of the window (or in any of the other windows as well). This will add your changes to the database.

Congratulations, you have just identified the function of a new gene that has never been seen before!