Dealing with DNA and protein sequences can be difficult without the aid of software. After the advent of computational biology and bioinformatics, several DNA manipulation programs have flooded the cyberspace, especially web-based free tools. Though some of these applications are handy and efficient, they do not include all the features required by a molecular biologist. Clone Manager Suite from Sci-Ed Software is a comprehensive software package with an integrated set of tools. It provides applications for enzyme operations, cloning simulation, graphic map drawing, primer design and analysis, global and local sequence alignments, similarity searches, laboratory-sized sequence assembly projects, virtual cloning, mutagenesis profiling, and more. The versatility of the software is realized through its diverse applications and visualizations.
This Windows®-based package comes integrated with three programs: Clone Manager, Primer Designer and Align, each of which is dedicated for a specific purpose. Clone Manager Professional contains all of the features of Clone Manager Basic, but adds modules to provide additional capabilities. New DNA or protein molecules can be generated or imported from the clipboard. The molecule window has tabs for Map, RMap, Seq and Info providing complete and lucid visualization. Most useful among these is RMap, which gives a very flexible display of the restriction pattern of the supplied molecule. All the saved/open molecules are by default recorded in the Molecule-list for ready reference. The three fundamental operations: Simulated Cloning, Primer Design and Sequence Alignment, can be executed using the appropriate sub-features. Under cloning, one can either plan a complete cloning or plan each step: restriction digestion, modification, ligation, independently. The Cloning Wizard is really amazing with the options it has. It lets you describe your cloning objectives, review the list of possible solutions, and instruct the Wizard to construct the recombinant of your choice. Similarly, under primer design one can design PCR/sequencing primers against any given target sequence, analyze it, perform a virtual PCR and further analyze amplicons thus obtained. With the alignment tool, the user can choose between a multiple alignment and comparison or scan for similarity between two sequences. Within these features there are several sub-options to optimize the alignment (and accompanying graphics) as per the user’s needs. For example, multiple alignments can be done against a reference sequence or against each other.
Clone Manager reads files in GenBank, EMBL, FASTA or Clone Manager file formats, or sequence data in simple ASCII text files. For a publication or presentation, use an Enhanced View of the graphic map to customize a special molecule map where you can set individual styles, colors, patterns, and positions.
I’ve used Clone Manager for several routine applications. I have found it particularly user-friendly and efficient for designing specific and non-specific PCR primers, performing restriction analyses; analyzing data from automated DNA sequencing, and planning a cloning experiment (using virtual cloning). I would recommend the software for basic to higher-end molecular biology applications.