Overview

This group of stand-alone sequence manipulation and analysis programs from Sci-Ed Software can be linked together within a central program "hub" to form a remarkably flexible and easy-to-use package suitable for comprehensive molecular analysis. Clone Manager 5 provides cloning simulation; restriction-enzyme mapping, including the generation of graphic maps; ORF identification; detection of repeats and dyad symmetries; protein translation; basic hydrophilicity analysis (Kyte and Doolittle or Hopp and Woods methods); and secondary-structure analysis (Garnier-Osguthorpe-Robson method). Primer Designer adds the ability to select suitable primers for sequencing, PCR, or for use as oligonucleotide probes. Align Plus provides several methods for aligning and comparing either DNA or protein sequences. Multiple sequence alignments can be performed, as can rapid scans for similarity, either on sequences located on your computer or in public databanks such as GenBank, Unigene, or the Protein Information Resource. Two sequences can be compared to identify frame-shift mutations or sequencing errors. An additional database utility can be used to organize and store information about molecules or primers.

How Long Did It Take to Learn to Use It Productively?

About a day per program/component.

Product Quality

Customizability

Some components are highly customizable. Specifically, criteria used for primer selection can be altered easily to reflect user preferences. Otherwise, customizing comes via the multiple options provided for menu-driven analyses.

Ability to Program in Scripts, Add Extension Modules, etc.

As previously mentioned, when two or more of these programs are installed, they integrate within the Sci-Ed Central hub to appear as a single program with increased functionality.

Ability to Import and Export in Different File Formats

Sequence can be pasted from the clipboard or loaded from GenBank, EMBL, or ASCII files. Export is limited to the generation of either ASCII files or a more informative GenBank-like file with standard identifiers. Graphic maps can be copied to the Windows clipboard for use in other Windows applications. Alternatively, graphic maps can be exported as a Windows metafile.

Useful or Unusual Features

The publisher is justifiably proud of the seamless way in which the individual programs combine within Sci-Ed Central, the program hub. Individual sequences are displayed in an onscreen Molecule Viewer window. This window allows immediate access to the map, restriction map, and sequence, and to miscellaneous features and molecule data. A similar format is used to display information related to primer selection and sequence alignments.

The programs contain "wizard" protocols that are intended to guide novices through the most complicated analysis protocols. Of particular note, the Cloning Wizard, a feature of Clone Manager 5, suggests strategies for cloning projects with attention to selected inserts, vectors, and restriction maps, and accepts the user's preferences for procedures such as directional cloning, insert orientation, and chosing an enzyme supplier. Even experienced users will benefit from a program that uses the comprehensive restriction-enzyme database to find creative cloning solutions such as complementary ends. This database is derived from REBASE, and can be downloaded from the REBASE Web site to keep it up to date. Within Primer Designer, similar wizards assist in the selection of appropriate primers for RT-PCR and for the design of oligonucleotides for LCR. Primer Designer also discriminates in the selection of primers for PCR or sequencing or as probes. Additionally, the Mutagenesis Profile feature of this program enables the alteration of primer sequences and their reanalysis. This feature can also be used to identify "almost" enzyme sites in target sequences. General features include "work boxes," which are the equivalent of favorites in Windows 95. These operate as shortcuts to folders that are regularly used. A central repository of critical files (common lab vectors, primer lists, shared sequencing projects, backups) within the computer or located on a network server can be designated. This feature is particularly useful to individual research groups that archive, share, and manipulate sequence.

The intuitive design is a particular strength of this software. All three programs provide an interface strikingly similar to the "on paper" approach biologists would take to perform these tasks. The cloning simulation of Clone Manager 5 is easily regulated, and molecule fragments are assembled in a manner instantly recognizable to those more accustomed to outlining such manipulations in the page margins of an enzyme catalog. The same natural feel is also reflected in Primer Designer and Align Plus when presenting the outcome of analyses in both graphic and sequence format. Novice cloners or individuals who rarely need to use such software will feel in control of parameter selection rather than at the mercy of the preprogrammed defaults.

No major limitations could be detected within these programs. The stepwise menus provided to assist users in carrying out some of the more complicated analyses seem restrictive when used repetitively. Similarly, establishing new sequence files seems to require more information than one might want to bother with for bits of sequence of unknown significance or relevance.

Comparisons with Similar Software

Having used Clone Manager 4 loyally for many years, through the Windows 3.1 version and onward, I was predisposed to favor a good upgrade of this program, but I was also very impressed with both Primer Designer and Align Plus. Although many primer-selection and alignment programs are freely available via the Internet, the individual Sci-Ed programs are efficient, flexible, and so highly customizable as to make them worth the financial outlay. Once integrated into the Sci-Ed Central hub, the programs rival the output of Omiga or Lasergene.

Technical Support and Documentation

The provided manuals are well written and aid initial interaction with the programs. The online help is adequate. Usefully, Primer Designer's online help includes a section entitled "Basics of Primer Design Theory," which is a discussion of the most important concepts in primer design. Align Plus also has sections that discuss the theory underlying the algorithms used. These sections are useful tools for inexperienced users wishing to modify or customize in a rational manner.

Target Users

Novices through experienced users are likely to find these programs useful. They are particularly helpful for individual users who are approaching the mechanics of molecular biology, such as cloning or sequence analysis, from some other discipline. The combination of stepwise menus with sound theoretical information allows specific, immediate needs to be addressed while shortening the learning curve for future endeavors. Individuals who have only occasional needs for such software also benefit because the familiarity of regular use is not essential.