gene construction kit
flexible formatting & manipulation
DNA can be represented and manipulated in either graphical or sequence/text modes - with any formatting or sequence manipulation changes made in one view, automatically being applied to the selection in the alternate view. Users have complete control over the display in either mode. Segments can be selected in either mode and cut, copied, or pasted. When a selected segment is cut or copied, the ends are defined by the sites used to delimit the segment. 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, GCK utilizes a unique "ligation dialog" to assist users in adjusting the ends for compatibility. 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 the manipulations warrant it.
graphical display
In the graphical 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. 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. GCK features a magnification tool - which 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. Zooming in or out presents views of the construct at any level of magnification, allowing viewing, editing, or printing at any level of detail. A scale can be shown if desired.
sequence display
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. Amino acid sequences corresponding to either DNA strand optionally may be shown - in one letter or three letter code. Font, size, style, and color may be defined for any segment of the sequence. Nucleotides can be grouped in 3s, 10s, or any other number desired (ex. coding regions can be grouped in threes, general listings can be grouped in tens, octamer motifs can be grouped in eights, etc). Frames can be placed around specific sequence motifs. Line breaks may be inserted at any location. Regions of Interest can be shown as arrows.
illustration window
Gene Construction Kit also features a separate file window called an Illustration window that provides an ideal environment for assembling figures for publications, posters, project planning charts, or slides. Multiple constructs, gels, or sequence listings from GCK can be displayed simultaneously in a single illustration window, and can also be adorned with simple graphical elements, or external images, simplifying the design and management of multi-part cloning and sequencing projects. Complex construction projects can be stored as Illustrations and updated as new constructs are assembled, providing a simple way of tracking complicated projects. Explanatory text can be added at any location in the illustration and attributes (font, style, size, and color) can be assigned for each individual character of the text. Drawing tools available include lines/arrows, filled or empty rectangles, round rectangles, and ellipses. Any construct in the Illustration window can be edited 'in situ' as a construct.
