Reviewed by
(Issue 4; posted March 21, 1997; archived April 4, 1997)
Test Platform:
Power Macintosh 6100/7200 and 8200 series running Mac OS version 7.5
Overview . Program Features . The Bottom Line . System Requirements . Purchasing Information
The Gene Construction Kit is a powerful package that is primarily intended as a tool for designing and managing complex plasmid construction projects and assembling DNA sequences for use in DNA analysis programs. DNA sequence elements are presented graphically and can be manipulated with standard cut, copy, and paste commands. During each process, the program automatically adjusts the underlying sequence files to reflect changes in restriction sites, orientation, and keeps track of the history behind each individual DNA fragment. A set of drawing tools is included that allows users to create detailed illustrations of plasmid constructs for posters, slides, or papers.
As complex constructs are built by cutting and pasting DNA segments from one construct to another, a chronograph keeps track of any given DNA segment. The user can view a construct either as a text sequence, or as a linear or circular graphic. Virtual electrophoresis patterns for different constructs are easily generated for comparison with actual lab results, and this function can include partial digests. Each segment can have user-defined attributes such as thickness, pattern, shape, direction, and color. Restriction sites can be marked using one or more completely editable and expandable enzyme lists, and comments can be added to any part of a construct: DNA segments, marked sites, regions, or even the whole construct. Up to 32,000 characters may be stored in each comment field. Comments can store literature references, growth conditions, storage locations, or other pertinent information about the construct and can function as an electronic notebook.
The program automatically monitors sticky ends generated by restriction enzymes. The program gives a helpful warning if the user tries to paste together incompatible ends. Special paste options allow a sequence to be inverted and/or to have the ends filled or trimmed before pasting. Perhaps the most useful function of this program is that it automatically keeps track of the history for any segment of DNA in a given construct. This information can be used to track a series of steps in a construction project, so planning for complex enzymatic manipulations is easy. Constructs can consist entirely of Ns into which restriction (or other) sites can be placed, allowing for construct manipulation even in the absence of DNA sequence. As sequence data becomes known, the Ns can be replaced by the known DNA sequence.
Illustrations produced in the program can contain multiple constructs, diagrams of predicted electrophoresis gels, sequence listings, legends, and other graphics, as well as free text. Illustrations can be up to 11.6 meters (38 ft.) square. Complex construction projects can be stored as illustrations and updated as new constructs are assembled, providing a simple way of tracking complicated projects. Images generated by the Gene Construction Kit are saved as PICT files for further editing in a drawing program.
Searching for individual files or sequences is accomplished by matching key words in the comments or sequences. Searching is straightforward, and individual folders or an entire disk may be searched. In addition, the exchange of sequence information between the Gene Construction Kit and other programs is straightforward. Sequences generated in the program can be saved as DNA Inspector files or as formatted or unformatted text files. DNA Inspector files, as well as GCG, EMBL, PIR, GenBank, and files of other formats can be read directly into the Gene Construction Kit along with associated comments.
The Bottom Line
This program is an excellent addition to any lab that does a lot of cloning. While providing the capabilities of a powerful construction project designer and a DNA illustration tool, The Gene Construction Kit features an easy-to-use interface for manipulating sequences without concerning the user with underlying details. Users can evaluate cloning approaches before experiments are done, and the systematic manner in which the program tracks DNA fragments is a great organizational asset. When a group uses this program regularly, it will greatly improve the organization of the all too often disorganized lab records used to create complex DNA constructs. Thankfully, the intuitive interface allows even inexperienced computer users to begin with minimal training.
The Gene Construction Kit is available for all current Macintosh computers (starting with the Mac Plus) and is completely compatible with System 7.
About $550 from Textco, Inc., 27 Gilson Rd., West Lebanon, NH 03784. By phone or fax: (603) 643-1471. E-mail: info@textco.com. URL: http://www.textco.com.
Al Aplin received his Ph.D. in biology at Indiana University and is currently a postdoc in North Carolina.
