Overview

Figure 1

OMIGA is one of the most popular data presentation and analysis software packages for molecular biologists on the market. OMIGA excels in its use of the Windows Explorer interface: with it you can organize data of any format into a hierarchical form (figure 1) using external viewers such as RasMol. You can import almost any kind of sequence data into OMIGA, with the notable exception of electropherogram data from automated sequencing machines.

Figure 2

OMIGA includes a battery of different algorithms for nucleotide and protein analysis, including sequence alignment, restriction enzyme analyses, primer searches (to find primer pairs for PCR or sequencing), and sequence motif searches. You can search your DNA for open reading frames; calculate proteins' amino acid composition; find transmembrane domains; assess protein hydrophobicity, antigenicity, and flexibility; and predict secondary structure. Various other data can be integrated and viewed in a feature map (figure 2). In this way, DNA sequences can be viewed along with any other data you're interested in. For example, you can look at open reading frames along with a restriction map, amino acid sequence, and so on.

OMIGA offers all these features in a very appealing and user-friendly format. Although a range of advanced customization options are available for experienced users, to avoid confusion, complex settings are kept out of sight unless the user activates them. Overall, OMIGA is fast, reliable, and feature-rich, offering both basic and highly advanced features that perform quickly and accurately. It should appeal to anyone working with nucleic or amino acid sequences.

Available platforms	Windows 95, 98, and NT
System requirements	CD-ROM drive, TCP/IP connection, SVGA Windows 95/98 66 MHz 486 (Pentium recommended) with 16 Mb RAM (32 Mb recommended) Windows NT 4.0 133 MHz Pentium with 32 Mb RAM
Test platform	300 MHz Pentium II with 128 Mb RAM, running Windows 98
Price	$1,995 commercial $1,495 academic (see vendor information)

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

After a few hours of going through the "Getting Started" booklet, and going through more specialized features of the program, I could confidently work with the program without relying on the manual.

Product Quality

Customizability

User can modify almost any data in OMIGA. For instance, you can both edit built-in databases and create new ones for restriction enzymes, proteolytic agents, and nucleic acid, protein, and gene-associated motifs. Additionally, all search results can be filtered using the Windows Explorer-like interface in feature maps.

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

None.

Ability to Import and Export in Different File Formats

Any kind of data, from figures created in another program to crystal structures, can be added to a project so long as a separate application is available to handle the data for external viewing. Additionally, OMIGA provides native support for almost every kind of sequence data (see table), with the notable exception of ABI file format (see Comparisons with Similar Software, below).

Limitations

See Comparisons with Similar Software.

Comparisons with Similar Software

Most programs of the same class as OMIGA (such as DNAStar's Lasergene) are constructed of modules: the program suite is split into many programs, each of which performs a specific task. These modules often need to exchange data with each other, which can sometimes be tedius and confusing. OMIGA is set up differently, with all functions integrated into a single program. Although this might sound like a recipe for an application too complex for most users, it is not. The simple and appealing layout of the Windows Explorer-like interface is extremely well integrated with the various available functions.

The weakest feature of OMIGA relates to its inability to work with ABI files. As recognized by the makers of Lasergene, automated sequencing machines are very important for the modern molecular biologist. In the current version of OMIGA, you cannot work directly with the data generated by these machines (electropherograms). The only way to work around this is to have a separate program to align your ABI datafiles, and then export the results to OMIGA. Set aside, OMIGA is without doubt one of the most feature-rich programs of its class, one of the fastest, most reliable, and easiest to work with.

OMIGA version 2.0 is scheduled to be released this year. It will have a variety of new features, including the ability to search and retrieve sequences in the NCBI Entrez and BLAST databases, analyze user-specified sequencing and PCR primers in a template-independent manner, and perform dot-matrix analyses (DNA-DNA, protein-protein, and DNA-protein). Unfortunately, the ability to read ABI files will not be included in OMIGA 2.0, but this feature is on the list of upgrades planned for the future.

Technical Support and Documentation

OMIGA's technical support is excellent and free of charge. Users can choose to fill in a Web-based form describing their problems or to send email to support addresses in either the United States or England. Answers, including detailed solutions, are returned by email within 24 hours, except on weekends. There are also telephone support lines in the United States, England, and Germany, whose consultants provide instant help.

Documentation comes in different formats. A detailed installation booklet aids in setting up the program. New users can choose between the online "Quick Tour" or the more detailed "Getting Started Booklet" to learn the basics of using OMIGA. There is an online copy of the user manual, which is very handy for searching for keywords or accessing help when the hard copy manual isn't at your fingertips. Finally, detailed context-sensitive help is provided in the standard Windows help format.