GeneCoder Overview

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GeneCoder is a comprehensive molecular cloning and sequence analysis software package. The GeneCoder user interface is managed by a single centralized window providing access to views, database, and tools. This centralized window is compartmentalized into 3 distinct regions:

The Sequence view is located on the right side of the main frame and is the main way to view sequences. Sequences are opened in tabs, each of which represents a distinct sequence file. Different sequence types have different ways to view the sequence, accessible via the drop down menu in the upper right. For instance, DNA sequences can be viewed by default in 3 ways: in the editor (default), as a restriction map, and through a restriction digest panel. Many of these panels are interactive, for instance one can select sequences by dragging the mouse, or perform operations by right clicking on a particular area. Further, GeneCoder can be further customized and extended via the plugin API

GeneCoder View

GeneCoder application with a single plasmid sequence opened to the restriction map view. The blue box indicates the drop down menu capable of switching between views.

The Database is located in the upper left side of the main window and allows you to quickly access and organize your sequences. Double click a sequence, or drag the sequence onto the view panel to open the file. Right clicking on the database panel allows one to create sequences, browse the files through your operating system, open, rename, delete, etc...To save a file, go to File->Save (or save as, command-S) and you will be prompted to choose the location to save the file.

GeneCoder Sequence Database

GeneCoder application indicating the database panel outlined in green.

The toolbox, located in the lower left of the GeneCoder main window is the location where sequence analysis and manipulation can be performed. The tools are organized by type and can be run by double clicking the tool, or clicking the run/arrow button just below the toolbox. Some tools will only be active when the appropriate sequence type(s) are opened or selected. Tools can also be accessed via the tools menu. The toolbox provides many common tools to analyze and manipulate sequences as well as access public databases. Further, the toolbox can be extended and tools added by utilizing the GeneCoder plugin API

GeneCoder Toolbox

GeneCoder application indicating the toolbox location highlighted in green.

GeneCoder enhances the workflow of molecular cloning by allowing quick and easy sequence analysis and manipulation.

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