Silent Mutations
Silent mutations are point mutations in a DNA sequence that do not alter the coding information in that DNA sequence. GCK® allows you to create new restriction sites by silent mutation as well as to remove existing restriction sites through silent mutation.

Sophisticated Restriction Site Marking
GCK provides you with a complete list of all known restriction enzymes with which to work, while also providing lists containing only commercial enzymes or enzymes sorted by recognition sequence lengths. Enzymes sites can be marked by how many times they cut, by the kind of cut they create (5', 3', blunt), or by whether or not they cut within a specific segment. This allows sophisticated searching such as mark all unique blunt end cutters that cut only within a selected segment of DNA; or, mark all enzymes that cut more than 5 times, but only cut outside a selected segment.

Auto-Arrange Site Markers
Often when multiple restriction sites reside close to each other on the DNA, such as in polycloning sites, the site marker text overlaps. Using GCK's autoarrange feature, these sites can be arranged automatically so that none of the text overlaps. When a marked site is set to "autoarrange", it will do so every time the construct is manipulated either by changing the window size or cutting and pasting. You can even specify how you would like the auto-arranging to work. This assures you that the sites will be arranged in a visible and esthetically pleasing manner.

Listing Sites
In addition to marking sites directly on the construct, GCK also provides a text listing of sites. Listing sites produces a text output containing the enzyme names and the locations of all the sites and can be saved as a text file. Listing sites has the same flexibility as marking sites.

Selecting Marked Sites
Once sites are marked, they can be selected by the kind of cut they create. If you have a construct marked with many sites, you have the ability to select only those sites which are blunt ended or have 5' or 3' overhangs. This can facilitate cloning strategy planning.

Manipulating Site Markers
In addition to auto-arranging site markers, you also can place markers exactly where you want them to be. Each marker can be selected and moved one pixel at a time with the arrow keys. This leaves it up to you to decide where the marker should be located. In addition, it is possible to select any number of site markers simultaneously by using the mouse to drag a selection rectangle over those sites.

Find Open Reading Frames
GCK will look for open reading frames using any codon table you specify and will mark those regions automatically. These regions will show up as protein sequences in the sequence view of the construct.

Edit Codon Tables
The ability to find open reading frames depends on the use of codon tables. GCK comes supplied with a number of standard tables, but you still might like to create your own for special cases or specific organisms. The codon table editor allows you to do so.

Names for Generations
Using the chronography feature allows you to automatically track the history of your construct and to maintain different graphical and sequence views of the construct. In GCK, you can name each generation and provide comments to be stored with the generation. This makes it easy to annotate the construction process and then search your steps electronically later on.

Region Names in Construct Window
It is sometimes difficult to remember what each region in a construct represents. In GCK, you can choose to show the name of any region in a construct within the construct window. This can be set for each individual region.

Frame Segments of DNA in the Sequence Display
Frames are boxes that can be used to highlight specific features of a construct sequence. A frame can encompass the site markers, the sequence, and/or the regions of a construct. You can set the frame color and pattern.

One Letter Amino Acid Representation
GCK allows you to use either the three letter representation or the one letter representation for amino acids in the translated regions of your constructs.

Align Objects in Illustration Window
GCK allows you to select multiple objects in the Illustration window and align them vertically and horizontally.

Object Manipulation in Reduced View
GCK allows you to manipulate objects in reduced view to get the page layout exactly as you want it.