SnapGene is software that allows you to visualize and edit genetic sequences. This is extremely useful in a field like synthetic biology where existing sequences are combined to form new ones that allow organisms to perform novel functions.
There are a number of ways you can view a genetic sequence in SnapGene. The default view is the map which hides the letters in the genetic sequence to create space for visual features. These features allow you to see the reading frames of the sequences you have in your file, and highlights the parts of your construct that hold given sequences.
Clicking on show translate on the left adds some features that show the reading frames of each sequence. If the length and direction of the reading frames feature are the same as the length and direction of your gene’s feature, the gene will likely be transcribed correctly.
Other views can be accessed by selecting one of the options in the Views menu. These views allow you to see features included in your file, the restriction enzymes in your sequence, the actual characters in the sequence, and your primers.
The Features view, which is accessed by clicking on Views and selecting Features, shows some information about the sequences you have. This includes the number of base pairs, the number of amino acids and the molecular weight of the sequence in Daltons. This information is important for estimating the cost of synthesizing your sequence and is useful in a number of calculations.
The Sequence view shows the characters in the sequence is convenient when editing sequences because it allows you to pinpoint the critical locations in the sequence. The Sequence view also shows the features seen in the map view, and adds an extra feature, a red mark that indicates the stop codons of your sequence.
Restriction cloning is a method of editing genetic sequences by cutting them with restriction enzyme at suitable restriction sites. A number of cut sequences can be joined together with a process known as ligation. This process is performed in the lab following a given protocol. SnapGene allows you to simulate this process either by using the protocols it has available or creating your own.
There are a number of things to consider when applying restriction cloning, such as which restriction enzymes to use. This is of particular importance because you don’t want to use an enzyme that can cut somewhere in the middle of a genetic sequence. In addition, the combination of restriction enzymes you use determines how a genetic sequence will fit in a construct. This will determine whether or not it will be read correctly.