Overview

Primer Premier is a simple, straightforward, robust primer design program. The goal of the program designers at PREMIER Biosoft was to create functional software that performs a specific task, and to provide that software for a reasonable price. The main strength of Primer Premier is a simple interface that is effective and easy to learn. Whether one is designing primers for PCR, hybridization probes, or sequencing, Primer Premier provides the shortest path to the goal of an efficient primer. The researcher is not required to specify complex search and stability parameters to design an effective primer, as most conditions are defaulted to published optimal values.

If one chooses to take more control over primer design, then all the standard parameters like Tm, GC content, 3' end stability, and GC clamp can be modified. One can screen for repeats, sequence runs, dimers, and hairpins, all with different stringency. One can also check false priming by comparing the primers against a directory of sequences. Search results are easily viewed, giving positions of primers and product sizes. One can also examine graphs of %GC, Tm, and stability of 5-mers.

A useful feature of the program is a customizable restriction site search utility, which allows one to filter enzymes for cut length and overhang sequence. Another useful feature is the ability to search for sequence motifs from a list of 150 annotated motifs. Users can edit and expand both the restriction site and motif lists.

Primer Premier makes it easy to perform such tasks as creating degenerate primers or primers for multiplex and nested PCR. Once primers have been created, they can be stored in project- or user-specific databases and then printed on a faxable order form. One drawback of the program is the difficulty in exporting primer information from the database to other applications. However, one can print reports that contain most of the above information.

The ease of using Primer Premier is due in part to the multimedia tour that one can download from the Web site. The tour is free, it provides a good introduction to the main features, and it is an effective way to learn to use the program.

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

One to two hours. After taking the 15-minute tour and exploring the menu items, I was able to start designing primers immediately. For more advanced functions, up to one day of experimenting with different menus is required.

Product Quality

Customizability

Excellent. Complete control over all aspects of primer design is available if one chooses not to use the defaults. Parameters like melting temperature, GC content, 3' end stability, degeneracy, and GC clamp can all be controlled. One can screen for repeats, repeat runs, dimers, hairpins, and false priming, all with custom stringency. The restriction site database can be edited and expanded. A useful feature is the ability to filter for enzymes with very specific cut parameters, like overhang sequence and length of cut. One can also edit and expand the motif database, making the program a useful sequence analysis tool. Primer Premier also allows one to choose from a number of codon tables or even define one's own table for translation.

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

Primer Premier does not offer the ability to program in scripts, and there are no extension modules available. Upgrades are free from the Web site.

Ability to Import and Export in Different File Formats

Importing sequences is quite easy. GenBank files are automatically loaded, and Primer Premier has a versatile method for importing any other format. The program will open a plain text window of the file and ask you to click where the sequence starts. Any text before that is saved as a header to the file. You don't have to wonder if your sequence is in the correct format. I was able to open the file saved in either EditSeq, DNA Strider, or plain text format.

Exporting information about primers is difficult. There is a database that is designed to store primers for different projects, yet exporting information directly from that database is impossible. Reports can be printed displaying information about primers. However, there is no direct way to make that information available for any other programs.

Useful or Unusual Features

One nice feature is the ability to back-translate from a protein to a degenerate DNA sequence and to then perform degenerate primer design. Primer Premier has special parameters to search for an optimal degenerate primer. One can translate a sequence into a protein and back into DNA using a number of different codon tables. Additional tools to aid in sequence analysis are such features as restriction site mapping and motif mapping. The restriction site search is fairly standard, but there are some extras in this program, like the ability to filter the search to find specific lengths of recognition sites, specific overhang sequences, and even editing to create new sites or modify old ones.

The extensive list of motif sites is a noteworthy feature. The user can edit as well as expand this annotated list. Primer Premier also comes with a primer database function that allows storage of primers in different projects. These primers can be used to generate an order form that can be used for faxing a primer order.

The database function is the major limitation for my applications. I may choose 15 to 20 primers for a stretch of sequence, and I would like to have the ability to transfer information about those primers into a separate text file or to use the information in analysis programs on a different platform. The database in Primer Premier does not allow exporting of such information.

The interface for Macintosh is somewhat primitive: window-scrolling is jumpy in most views, making it difficult to home in on a specific sequence or to view sites as they pass in the window. In addition, tabbing to different fields is not available and no letters can be typed in the PO# field of the primer order form. The Macintosh version has no online help, and the database feature often crashed. It is obvious that not a lot of programming went into fixing bugs or handling errors in the Macintosh version of the software. The Windows version has a much smoother and bug-free interface. Windows 95/98 versions have some problems with conflicting software and operating system settings, but workarounds are available from the Web site.

Compared to programs like Oligo or PrimerSelect, Primer Premier has the advantage of being cheaper and easier to use. Of course, it is not as feature-rich as these other programs, but this is made up for by a more intuitive and easy-to-understand user interface. Compared to online primer design programs, Primer Premier is faster and has a better interface.

Technical Support and Documentation

There is little documentation for Primer Premier, primarily because little is needed. The intuitive design of the program makes it very easy to learn by simply browsing through the menus and windows. However, the manual is well written and organized, covering every function in a concise manner. Also included are clear discussions of the criteria that go into the design and analysis of an effective primer.

In the Windows version of the software, online help was quite useful and often context-based. Clicking on the help button in any window will take you to a discussion of the functions in that window. Online help is not available for the Macintosh version of the program. Technical support is freely available through email and phone. Support staff is helpful, attentive, and knowledgeable.

Target Users

Any researcher or laboratory with the need to design oligos on a regular basis. The lower price, compared to other more complex and feature-rich programs, makes Primer Premier a good value for labs on a budget.