The Gene Construction Kit® represents a breakthrough in interface design that allows graphic manipulation of DNA sequences in addition to providing sophisticated drawing capabilities. It is ideal for designing and managing complex construction projects or assembling DNA sequences for use in DNA analysis programs such as the DNA Inspector. It readily generates high quality black and white or color illustrations for slides, posters, or papers. All the figures in this flier were generated entirely by the Gene Construction Kit.

Manipulate DNA Sequences Graphically

As graphic sequence elements are manipulated, the Gene Construction Kit automatically adjusts the DNA sequence represented by the graphics. Every cut, copy, and paste operation performed graphically also occurs in the underlying sequence.

View Constructs Graphically or as Sequence
Constructs can be manipulated and represented in either graphical or sequence modes. One can paste a sequence into a graphical construct or vice versa. You have complete control over the display in either mode. The figure above shows an entire construct viewed graphically, with part of the sequence shown as text. Note that the colors are preserved in segments between the two views. Segments can be selected in either view and cut, copied, or pasted. Amino acid sequences corresponding to either DNA strand optionally may be shown. Selection of a segment in either view is accomplished by double-clicking on, or dragging across the segment. Selection in circular constructs is accomplished with a unique radial cursor which clearly highlights the selected segment.

Automatic Tracking of DNA Segment Ends


When a selected segment is cut or copied, the ends are defined by the sites used to delimit the segment. The Gene Construction Kit automatically monitors sticky ends that can be generated by restriction enzymes. Incompatible ends cannot inadvertently be pasted together. If such an attempt is made, the ligation dialog box shown above is presented. The "OK" button will not become selectable until the fragment ends are made compatible by dragging the arrows next to the sequences. Utilizing the special paste option allows a sequence to be inverted and/or to have the ends filled or trimmed before pasting, thus circumventing the ligation dialog if your manipulations warrant it.

Graphic Display Mode
In the graphic display mode, the construct can be displayed as linear or circular, and each segment of the construct can be defined and displayed in varying thickness, pattern, shape, direction, and color. Restriction enzyme sites can be found and marked automatically, and site markers can be automatically arranged.

Enzyme sites are selected from user definable lists which contain recognition sequences, cut sites, and comments that are to be associated with the site when it is marked on the construct. As shown in the construct at the above, sites can be displayed using either text or symbol. The text can contain the site name and/or the position (with user defined delimiters). Sites can be marked to be only within (or without) a selected region, or by 5', 3', or blunt cuts, or by the frequency of cutting. This would allow one to mark, for example, for all unique cutters that cut within a specific segment. The Gene Construction Kit has 48 different symbols and 36 different patterns to choose from. Linkers or adapters (selected from user definable lists) also can be inserted into the construct at any location. Regions of interest (coding regions, introns, exons, promoters, etc.) can be denoted with arrows or lines. Several layers of regions of interest can be displayed. Any segment of DNA between two marked sites can be selected, copied, cut, pasted, and edited.

Sequence Display Mode
In the sequence display mode, the construct is represented as a string of nucleotides, either single or double-stranded. Display options may be set to show/hide regions of interest, restriction enzyme (or other) sites, and nucleotide and amino acid positions at the start of each line. Font, size, style, and color may be defined for any segment of the sequence. Sequences can be grouped in 3s, 10s, or any other number you choose. Frames can be placed around specific sequence motifs.

You are not limited to monospaced fonts -- if you want to display a sequence in Arial or Times font, it will still align properly. Line breaks may be inserted at any location. Amino acid sequences can be automatically listed below the DNA in one letter or three letter code. Other Regions of Interest can be shown as arrows. Grouping of nucleotides in the sequence listing can also be defined -- thus, coding regions can be grouped in threes, general listings can be grouped in tens, octamer motifs can be grouped in eights, etc.

Magnification
Zooming in or out presents views of the construct at any level of magnification, allowing viewing, editing, or printing at any level of detail. The magnification can be set to a specific number of nucleotides/cm or can be set to fit the construct to the window or to the printer page. A scale can be shown if desired.

Chronography

The Gene Construction Kit automatically keeps track of history for any segment of DNA. This can be used to track a series of steps in a construction project as shown above. In this miniproject, a polycloning site is inserted into a stretch of DNA and then used for inserting a promoter and a gene. These steps can be carried out with simple cut and paste operations. When each segment is pasted it carries with it all of its chronography. Thus, when the previous generation is viewed, details of the inserted DNA are displayed. You can create up to 32,000 generations for any construct. Another use of chronography is to store alternate views of the same construct. Thus, one generation might show restriction sites, another the coding regions, another the transcripts, and yet a fourth generation might show the sources of each DNA in the construct. The ability to show any generation for any segment and to mix generations in viewing the same construct, provides a great deal of flexibility in displaying the information that is part of the construct while at the same time providing a natural way to keep track of the history of complex constructions. One never loses track of where a specific piece of DNA came from since previous generations of that segment are always available for viewing through chronography.

Generic Constructs
Constructs can consist entirely of N's, into which restriction (or other) sites can be placed. This allows for construct manipulation even in the absence of DNA sequence. As sequence data becomes known, the N's can be replaced by the known DNA sequence. Construct maps and gel electrophoresis patterns can be generated using generic constructs, which can function as function as working models.