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NCBI Resources: Tools

Contains information about the NCBI databases to be used as a teaching tool.

Sequence Viewer Tools

Sequence Viewer Tools allow you to annotate, export, and change the appearance of the sequence in the sequence viewer.  

Click on the Tools menu to see the options. These features are described below.

Tools Menu

Click on Tools to open the Tools Menu

We'll discuss these options in turn.

Flip Strand

Flip strand allows you to view the data in the reverse complement orientation. 

Before Flip Strand

After Flip Strand

Notice that both the gene cartoon (arrows indicate direction) and the numbers on the ruler are flipped. 

Sequence Text View

Sequence text view pulls up the nucleotide sequence along with translations of any genes in view. It also has a flip strands and go to position tools. You can also choose whether you want the translation annotations displayed. 

BLAST and Primer search

You can pull the sequence you're looking at in Sequence Viewer and pull it into BLAST or primer BLAST using this option. It will enter the unique identifier for the sequence as your query and autofill the range that you're looking at in the viewer. 

Go To

Go To lets you pick a specific base position to go to, and gives examples of how to format the query. 

Make sure to look at the allowable range formats.

Set New Marker

Markers are kind of like bookmarks for your DNA. You can give your marker a name and specify a position or range relative to the sequence ruler. Selecting Lock Marker will hold the marker in one place. If not, you can drag it around as you zoom and pan along the sequence. 

Once a marker is set, it will appear on the ruler. Hovering over the marker name will pull down a menu allowing you to modify, lock, or remove the marker.

Selecting Marker Details will allow you to see a list of all your markers.

Download

You can also download the sequence in a variety of file formats

Search

Search, aka Find on sequence, can work in the same way as Go To, but it can also search of the names of features, like gene names, SNPs and the like. 

Set Origin

Set origin allows you to select a base you'd like to number against. For example, you could set it to the base first base in a gene prediction. This will open a new ruler below the one for the whole sequence.

Before Set Origin

After Set Origin

Now you know the base positions relative to the entire sequence and your gene of interest. 

Note the new ruler below the regular ruler, and also that anything to the left of the new origin is in red. This indicates that it's 5' of the origin. The numbers on the ruler in the red space are NOT marked as negative on the display.

Add New Panel

Add new panel opens up a second viewer beneath the original so that you can see different views of the same sequence. The panel initially shows the whole sequence, but you can zoom and pan or search to get to the location you want. 

For example, you can look at a whole gene sequence and zoom in on the start of the transcript at the same time:

Add new panel on range works similarly, but instead of viewing the whole sequence, it stays zoomed in on the part you're looking at in the first panel.

Use the x in the upper right corner to remove panels.