Sequence analysis tools

When looking at a sequence, you will be able to use several sequence analysis tools that we have made available to you. Under the "Tools" menu, you will find the restriction enzymes manager and the digestion simulator.

Restriction enzymes manager

Opening up the restriction enzymes manager will display two lists of enzymes. On the right you will find all the enzymes whose cut sites will be displayed if you click the ‘show cut sites’ button, and on the left side you will find a list of available enzymes. You can scroll through some common groups, such as BioBrick, BglBrick, and so on. Let's say you wanted to only view cut sites for the "BioBrick enzymes" group. Then select that group, get rid of all the enzymes in your current group, and click the add all button. Now you can see that the enzymes appeared on the right. You can customize the group by adding enzymes from other lists if you so desire. To save this group for later use, click 'copy group,' and enter a name for the group to be saved. Then you will be able to load this group of enzymes later.

Digestion Simulator

Another tool available to you is the digestion simulator. This will simulate the results of a gel digest on our sequence with the selected enzymes. The interface to the digestion simulator is similar to the restriction enzyme manager. On the left you have a list of enzymes that are available to simulate digestion with, and on the right there is a list of enzymes that are currently being used to simulate the digestion. As in the enzyme manager, you can change lists and search through available enzymes.

After simulating a digestion with a group of enzymes, you will see the results of the digestion in this right panel. These results will show the expected bands corresponding to each cut site. If you mouse over a band, you will see the name of the enzyme responsible for the cut site. You can also change the ladder to be used.

Other tools

Under the edit menu, you will find tools for selecting, finding, and altering your sequence. We have familiar features like cut, copy, paste, and undo and redo. You can also toggle the "safe editing" mode, which would warn you if you try to change the sequence of an annotation. If you try to delete a base in a feature, it would pop up a window asking you if you want to remove the feature, or keep it there in its altered state.