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SOFTWARE REVIEW |
Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
Key Words. Sequence analysis • DNA drawing • Cloning
Correspondence: Darryl Nishimura, Ph.D., University of Iowa, Department of Pediatrics, 4181D MERF, Iowa City, Iowa 52242, USA. Telephone: 319-335-9315; Fax: 319-335-7588; e-mail: darryl-nishimura{at}uiowa.edu
INTRODUCTION
Working with artificial DNA constructs is an integral technique of molecular biology. The organization, analysis, annotation, and presentation of the data associated with such constructs can be very tedious and time consuming. Thus, many software packages have been developed over the years to address these needs. Such packages cover a wide spectrum in terms of features, program usability, and price. They range from freeware or shareware packages that perform a limited set of tasks to commercial products that are feature-rich and expensive. In 1998, Redasoft Corporation released their first product, Plasmid, a program that allowed researchers to draw genetic maps. User feedback prompted Redasoft to add sequence analysis and cloning features to the program. In September 2000, an upgrade to the Plasmid package, Visual Cloning 2000, was released. Visual Cloning 2000 sported a user-friendly interface, detailed graphic capabilities, and integration with the Internet. Both of these products have been reviewed previously [1–3]. This review examines an upgrade to the Visual Cloning package, Visual Cloning 3.
INSTALLATION
Visual Cloning 3 is available from the Redasoft Website as a time-limited (30-day) fully functional demonstration program. This allows prospective users to work with the program on their own data to see if it will meet their needs. Some basic contact information is requested before the download. The installation on the machine used in this review proceeded quickly and flawlessly. To continue using the program after the trial period, a digital unlocking key must be purchased from Redasoft. The recommended system for running Visual Cloning 3 is a computer with a Pentium III processor, 256 MB of RAM, and Microsoft Windows XP Professional. Microsoft Internet Explorer 5.0 or above must also be installed on the computer. The minimum system requirements are a computer with a Pentium 133-MHz or higher processor, 24 to 128 MB of RAM (depending on the operating system), Windows 98 or higher, roughly 10 MB of hard disk space, and a monitor with 800 x 600 resolution or higher and 256 colors. Internet access is also required to use certain features of the program. The program displays a lot of information, so a large (at least 19-inch), high-resolution monitor would greatly facilitate the user experience. Visual Cloning 3 is only available for Windows at this time.
PROGRAM OVERVIEW
Visual Cloning 3 has been developed with the aim of creating a powerful yet easy-to-use DNA drawing program. Most users will have no problem in getting started with the program, because the user interface is basically a modified Web browser. A column of seven buttons on the left-hand side of the screen calls up different areas of the program. The program displays information in a single area to the right of the navigation buttons. Several windows of information can be displayed simultaneously. When multiple windows are displayed, they are automatically sized to fit into the available space. It should be noted that the program displays a lot of information, so it would be advisable for prospective users to use the largest monitor that they have available. This review was performed on a machine with a 15-inch screen, and a great deal of manipulation of the display windows was required to make efficient use of the program.
Reflecting its design as a DNA-based graphics program, the program allows the user to create visually appealing illustrations of both circular and linear molecules. Such diagrams would be very difficult to create with generalized graphics programs. Over the past few years, additional features have been added to the program in response to user requests. Thus, the ability to analyze sequence and carry out virtual cloning experiments has been implemented and enhanced. A great variety of DNA and protein analysis tools is available on the Internet for use by the scientific community. Thus, one of the most significant improvements to the program was its integration of Web-based tools a couple of years ago. This approach could have some potential disadvantages, because there is no guarantee that the free service will continue to be offered in the future.
SEQUENCES MODULE
In this area, the user is able to load a DNA sequence into the program. There are three sources from which a DNA sequence can be obtained. A sequence may already be saved as a text file, or it might exist on the Windows Clipboard. A sequence can also be imported from a Website on the Internet. Links are given for GenBank (National Center for Biotechnology Information [NCBI]), European Molecular Biology Laboratory (European Bioinformatics Institute [EBI]), or Redasoft’s Cloning Vector Search Engine. The Web address (or URL) for other sites can be entered manually. An advantage to using one of the three predefined Websites is that any annotation that is available for the sequence is automatically imported and displayed. Visual Cloning 3 is not currently capable of working with sequence files generated by automated DNA-sequencing instruments unless the file is provided as an American Standard Code for Information Interchange (ASCII) representation. A list of all of the sequences that have been stored in the program is also accessible from this section. This allows the user to quickly access any sequence that has been saved previously. The sequences are listed in a tabular format, and the order in which they are displayed can be sorted by clicking on the column headings (Document Name, Creation Date, and Modification Date).
ANALYSES MODULE
This portion of the program allows the user to conduct various types of analyses on a DNA sequence to characterize and annotate it. Analyses that are available include the following: Restriction Analysis, Polymerase Chain Reaction (PCR) and Hybridization Primer Design, Open Reading Frames Search, Motif Search, Basic Local Alignment Search Tool (BLAST), and Multiple Sequence Alignment. A brief summary of each area is presented.
In the Restriction Analysis section, options are available for the selection of different restriction enzymes. Two predefined enzyme sets are included, all enzymes and commercially available enzymes. The user can also define additional groups as needed or apply a filter to select enzymes that meet specific user-defined requirements. Recognition sites for each enzyme selected are shown in both a graphical map and a text-based sequence view. For each enzyme, additional information is available such as isoschizomers, other enzymes with compatible ends, and links to commercial sources for that enzyme.
The PCR and Hybridization Primer Design section allows the user to identify suitable primers for these types of experiments. The user is able to specify some of the parameters that are used for making the primer selections. Summary statistics of the primers that were considered are returned in a tabular format. The primers that are selected can be displayed both graphically and in the text-based sequence view. Links to commercial oligonucleotide suppliers are given in the primer details section, although these are mostly links to the homepages of each company. At the time of the review, some of the links were not functional.
The Open Reading Frames Search section allows the user to examine any or all of the reading frames for open reading frames (ORFs) that are larger than a user-specified minimum number of amino acids. The genetic code to be used can also be specified. All ORFs that are identified can be viewed both graphically and textually. Furthermore, the ORFs can be selected for BLAST analysis or examined with one of several tools from the ExPASy Website. Visual Cloning automatically transfers the sequence for the selected ORF to the Web submission form associated with each analysis.
The Motif Search section allows the user to screen the DNA sequence with a user-defined DNA motif. The BLAST section allows the user to BLAST the DNA sequence against the DNA databases at the NCBI Website. Either the entire DNA sequence or a user-specified range can be examined. Last, the Multiple Sequence Alignment section allows the user to submit two or more sequences for a ClustalW analysis on the EBI Web server.
CLONING MODULE
This module allows the user to carry out virtual cloning experiments. A fragment can be either inserted into or deleted from a vector. The user can also edit a DNA sequence directly. The sequence that is to be inserted can be obtained from one that is already loaded into the program or can be copied from the Windows Clipboard. The user can specify the location of the insertion or deletion by marker (restriction enzyme site) or region (annotated region) or by directly specifying the bases that are to be used. An insertion can either add sequence to the vector or replace some of the target vector sequence. When inserting or deleting sequence, the program checks to see if the ends that are created are compatible. If not, the user is given a choice to either fill in an overhang or to degrade it. When performing a cloning operation, all analyses for the selected vector are deleted. This is inconvenient when one wants to reuse the same vector for another experiment. It would be useful if the user could duplicate a sequence and the associated analyses before performing a cloning function or if the analyses were retained.
EXPORT MODULE
The Export Module allows one to export a sequence map to a graphic file for use in other programs. The following file formats are available: BMP, GIF, JPG, PNG, and TIF. The images can be exported at low, medium, or high resolution. The JPG format also allows the user to set the quality of the JPG image. There are also instructions on how to export a map as an encapsulated postscript (EPS) file. The maps can also be copied to the Windows Clipboard as either a Windows metafile or as a bitmap. Maps can also be printed out from within the program. Sequences can be copied to the Clipboard, printed, or saved as HTML.
OTHER MODULES
The program has three additional modules. The Start button pulls up an introductory page that contains a few helpful links. The user can start working with a sequence, learn more about the Visual Cloning package, learn more about Redasoft, or contact the company. The Workspace button takes the user to an area of the program in which the map or sequence is displayed in the entire working window. In other modules, the map or sequence has to share space in the window with another pane that is used to guide the user through the task that is being performed. On smaller monitors, this leaves little space for viewing the results. The larger display space makes it much easier to edit and modify maps and sequences.
The Internet button takes the user to a basic Web browser. This area of the program is also used by some of the other modules. For example, when one is importing a sequence from a Website or performing a BLAST analysis, this browser provides the access to the Internet that is required. One inconvenience that was noticed during the review was that it was not possible to go back to the page that originally called the browser. For example, if one is performing a BLAST analysis of a few ORFs, the browser is needed to access the NCBI BLAST Website. However, there was no easy way to navigate back to the Analyses window before being transferred to the Internet window. The entire ORF analysis had to be repeated.
MISCELLANEOUS ITEMS
Single-user licenses are available for $675 for academic and nonprofit organization users and $1,375 for commercial users. Additional volume and site license discounts are also available. Upgrade pricing is available for users of earlier versions. Upon purchase of the license, the user is sent a digital unlocking key to convert the demonstration version to a licensed version. A CD-ROM that contains a backup copy of the program is also sent to the user. Licensed users are entitled to free technical support by e-mail as well as upgrade pricing for future versions of the program. One issue to consider is that many of the tools provided in the program are hosted by Websites that have no affiliation with Redasoft. Therefore, continued access to these tools requires that Visual Cloning be updated should an interface change at the remote site disable the current method of access.
SUMMARY
Visual Cloning 3 is a useful and versatile program for annotating and generating graphical representations of DNA sequences. The program sports a user-friendly interface and a moderate level of drawing tools and sequence analysis features that allow the user to create detailed maps that can illustrate complex cloning procedures. Potential users should work with the demonstration version that is available to determine if the level of features provided in Visual Cloning 3 is sufficient for their needs.
CONTACT INFORMATION
Redasoft Corporation
E-mail: info{at}redasoft.com
REFERENCES
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