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Visual Cloning 2000

Gerard Hoehn, Ph.D., Johns Hopkins Oncology Center, 600 N. Wolfe Street, Oncology 3-109, Baltimore, Maryland 21287, USA. Telephone: 410-356-6431; Fax: 410-356-6428.

Visual Cloning 2000 is an integrative internet and DNA sequence analysis software package that also provides the user a graphical interface for easy-to-produce plasmid maps. The software is produced by Redasoft, a Toronto-based firm and is specifically designed for Windows users, which was a little disconcerting for this Mac user. However, I found Visual Cloning 2000 intuitively easy to use and understand. A feature advertised by the company is its commitment to using customer feedback for improvements to its software. In fact, the Redasoft Web page has a convenient link that allows the user to submit questions and feedback. Although I did not utilize this feature, it is somewhat reassuring that the company will listen to suggestions from its users.

In my estimation as a casual molecular biologist, the greatest advantage of Visual Cloning 2000 is that it creates an easy-to-use web-based browser for a variety of molecular biology resources. Of course, most of these resources would be freely accessible without the software package. However, Visual Cloning 2000 provides an organized compendium of many key sites that makes extracting relevant information that much easier. For this reason alone, I think Visual Cloning 2000 is a valuable asset to any lab. The main page of the software is the Redasoft Research Net that serves as a research portal providing access to a large number of cloning tools. From this page, there are links for sequence retrieval National Center for Biotechnology (NCBI) and analysis (ExPASy and CMS Molecular Biology Resource), online ordering of restriction enzymes and oligonucleotides, and useful tools and protocols (Double-twist.com protocol and quick access tables). These links greatly facilitate tracking down information, which is obviously a real timesaver. For example, importing sequence information from the NCBI database was very straightforward (no saving the sequence in a particular format so that it could be imported to your analysis software). Similarly, performing downstream analysis on the imported sequence was also quick and easy to accomplish.

The graphics for creating plasmid maps are very good and easy to use. Plasmid backbones are readily accessed and imported with the RedasoftUs cloning vector search engine. This feature greatly facilitates the generation of detailed vector maps. Restriction sites and other salient features can be readily added to your map. The graphics portion seems to be modeled after PowerPoint, making the features recognizable by most researchers.

In terms of the DNA analysis portion of the software, my opinion is that it is fairly ordinary; however, I think it is a valuable resource for a majority of routine applications. For example, once a sequence is imported (which is performed very handily through their browser links to most databases), restriction enzyme sites and open reading frames can be found, and polymerase chain reaction (PCR) primers and oligonucleotides generated. In Visual Cloning 2000, restriction enzyme analysis is queried against REBASE, a restriction enzyme database that can be updated. Sequences can be scanned for particular restriction sites or overhangs. Like other analysis programs, output is given by the enzyme name, site(s) on the sequence, and recognition sequence ends. For generating plasmid maps, it has a convenient feature that allows the user to add a particular site to the map. Another nice feature of Visual Cloning 2000 is that it will provide the names of companies that sell your enzyme of choice (particularly useful for rare enzymes), and has an easy-to-use, online ordering link. However, I found the manufacturer list to be incomplete. When I searched for several rare enzymes (one which we have purchased and used in our lab), the software responded by stating that there were no manufacturer's for this enzyme.

Imported nucleic acids can be translated to protein using the open reading frame program. Although Visual Cloning 2000 does not have any protein analysis tools per se, it has links to protein analysis databases such as ExPAsy. Analysis of polypeptides for protein characteristics (e.g., isoelectric point, molecular weight, amino acid composition), homology to other known proteins, and protein recognition sites are as simple as a click of the mouse. For novice and sophisticated users alike, the proteomic links make protein analysis very simple and easy to decipher.

PCR primers and oligonucleotide lists are also easily generated from the imported nucleotide sequence. This option has an advanced feature to allow the user to select parameters in choosing PCR primers (e.g., melting temperature, percent guanine:cytosine, etc.). Once primers are chosen, there is a direct link to order primers online from select companies.

Visual Cloning 2000 can be easily ordered and downloaded through the RedasoftUs Web page (http://www.redasoft.com). The corporate price is $599 (U.S.) and the academic price is $399, making it an affordable software package. In my opinion, Visual Cloning 2000 is a worthwhile and time-saving tool that would be beneficial for most labs.

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This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints/Permissions Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Hoehn, G. Search for Related Content PubMed PubMed Citation Articles by Hoehn, G.