gene construction kit

intuitive analysis tools

find open reading frames (ORF's)

GCK allows users to identify open reading frames based upon user defined parameters. The minimum ORF length can be defined, as well as whether the program should search one or both strands - or whether every ORF should begin with the bases 'ATG'. Additionally, users can change the codon table used in the analysis - should the sequence warrant a different table from the default.

PCR analysis

GCK integrates the popular Primer3 code, developed at the Whitehead Institute, into its PCR Analysis module to assist users in identifying primer pair candidates that flank a selected DNA segment. Users can choose default values for the primer parameters - or change items such as the primer melting temperature, salt concentration, or minimum/maximum size to meet any criteria.

The tool will scan the DNA sequence surrounding the region to be amplified and present a table listing all primer pairs that match the setup criteria.

Additional details are available for how each primer pair scored under the chosen attributes, and primers can be added to the construct as graphical forward and reverse indicators.

database searching

Gene Construction Kit features a simple interface for querying multiple online biological databases simultaneously. Users can search by keyword, DNA or protein sequence - and select various databases from a pre-populated list.

GCK takes care of the query format and processing, and once a query is complete opens a browser results page, with links to the completed search results on each database site. Simply click on the 'completed' link to open up a browser window displaying the results. By using the built-in Database Search feature of GCK, users no longer need to keep track of individual web sites, or worry about how to format query entries - simply enter the query term once, and all results are presented in a single location.

gel prediction

Using gel electrophoresis in the lab, it is often desirable to examine potential DNA fragment sizes from a restriction enzyme digest to facilitate the selection of appropriate construction pathways. Gene Construction Kit software features a digital simulation of gel electrophoresis, and allows patterns for any construct(s) to be viewed in a gel window. Standard sizes can be displayed, and gel lanes can be repositioned in the file through simple cut and paste operations. Users can choose to view the patterns as the simulated graphic, or a table listing the fragment positions and sizes. Additionally, GCK features a built-in algorithm to predict and display partial digests - which will help to mimic exactly what is seen in the real world application.