Using VectorNTI

If this is the first time that you have started vectorNTI you will be asked a bunch of questions about what to install. I suggest that you install everything to begin with, because you can always remove stuff later.

Note: All of the images below are shown small. To see a full-sized version, click on the image

When you first start vectorNTI you will be presented with a screen like this:

We will begin by focussing on the Explorer window as shown below:

Databases

The databases store all the sequence data. There are different databases for DNA sequences, protein sequences, oligos and so on. Click on the pull down menu to see the databases available

Each database can also contain sub-databases. You can have many different subbases, for example, one for each user. You can keep a shorter list of sequences in your own subbase. All the sequences will appear in the main database.

To add a new subbase:

Select New subbase from the table menu, and then enter a name for the sub base

You can enter sequences into your own database, either by dragging them from the main window, or by opening new sequences.

Suppose that you want to download a sequence from NCBI and enter it into your own subbase. These are the steps that you will follow:

1. Get the sequence from NCBI. This is covered in module 1. Save the sequence on your computer in genbank format. For this example I have downloaded the TNF-alpha sequence (gi number 54830)
2. Import the sequence into vectorNTI:
   
   
   • Select Import Molecule from Text File from the DNA/RNA menu.
     
   • Choose genbank (you did save it as a genbank file, didn't you?). Note that you can also import other sequence types from this menu.
   • Select the file that you want to open.
   • Select a sub base to save the DNA sequence in. It will appear in the subbase and the main database
     
   • Enter a name for the sequence. You can also enter other information by filling in the boxes in these menus.
     
   • Click OK and the sequence will be entered into your sub base.

Note: You can also download sequences directly from NCBI into vectorNTI either by choosing to open a sequence using VNTIMolDoc from the download manager or within vectorNTI. I am not going to describe these techniques here because this is the most important technique. It will allow you to enter sequences from a variety of sources.

In the next section we will take a look at, and customize, the vectorNTI display.