Overview

OMIGA is a comprehensive Windows-based program for analysis and manipulation of sequence data intended to support the individual scientist doing bench research. OMIGA complements the Macintosh-based MacVector, also published by Genetics Computer Group, a subsidiary of Pharmacopeia. A number of features have been added or enhanced in version 2.0. Major improvements include direct searching of the Entrez and BLAST databases, "one click" downloading of complete GenBank files, dot-matrix alignments of sequence pairs (nucleic acid or protein) and, as an optional extension, GCG Link (not reviewed here), which enables OMIGA to serve as the GUI for local installations of the Unix-based GCG Wisconsin Package.

User friendliness is a noteworthy feature of OMIGA. All tasks are performed in the unique integrated "project" format (See Useful Features), which has been carried over from previous versions. Sequences are manipulated in Sequence View, and the results of multiple analyses are displayed graphically either at large or nucleotide scale in Features View. Features, such as open reading frames or structural motifs from annotations imported with standard file formats or created by the user, can be displayed in both views. Coordination between the two views simplifies manipulations. For example, restriction fragments highlighted by a single click in Features View are also highlighted in Sequence View. When a fragment in Sequence View is pasted into the new sequence, restriction sites are correctly implemented, and features are incorporated into the new construct. Alignments are initiated by simply highlighting the files to be compared.

Multiple sequence alignments of nucleic acids or proteins use the Clustal W 1.6 algorithm. A number of parameters such as gap penalties, weighted mismatches, and divergent sequence delays can be controlled and saved as a protocol file. Colors in the aligned-sequence display can also be edited to highlight properties of the residues.

OMIGA can be used to design primers for PCR and sequencing. Version 2.0 provides the ability to test primers chosen by the user. The sequences of the primers are stored in a spreadsheet, and are not linked to the fragments displayed in Features View, making their identification a little cumbersome.

Protein sequences can be analyzed for potential secondary structures, defined as alpha helices, beta regions, turn regions, and flexible segments, by the Chou-Fasman and GOR II algorithms. Other local properties such as antigenicity, hydrophobicity, hydrophilicity, hydropathy, and transmembrane potential can be analyzed by a total of 14 algorithms. Chemical properties such as the pI of the isoelectric point and the charge at pH 7.0 are now provided along with several other physical measurements. Motif searching can be done on the desktop using the NASITE and PROSITE databases for nucleic acids and proteins, respectively. (See Limitations).

Overall, sequence manipulations with OMIGA are enhanced by the coordination between the Sequence and Features views and the new connection to the Web, and they make for a valuable tool that is conducive to efficient and accurate documentation of molecular biology.

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

I typically use MacVector, which operates on independent sequence files. Thus, the main hurdle to overcome was OMIGA's project environment. The Quick Start pamphlet (also provided as an online tutorial) and the Getting Started tutorial were both necessary and sufficient to enable me to design constructs and display them with features within a couple of hours. Reasonable proficiency requires some revisiting of the tutorials over the following few sessions. Other functions can be used as needed with a minimum of preparation.

Product Quality

Customizability

The built-in databases for the search routines can be modified, and the user can create new search items and/or parameters. Searches can be filtered in advance for certain parameters, such as the length of restriction sites, or the results can be filtered afterward for parameters such as the region to show or the number of cuts by an enzyme (See also below in Limitations). The content of the Features View is highly flexible: multiple types of features (restriction and proteolytic sites, open reading frames, genes, promoters, etc.) can be shown simultaneously.

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

GCG Link (See Overview) extends the functional capability of OMIGA.

Ability to Import and Export in Different File Formats

GenPept has been added to the previous list of file formats handled by OMIGA. OMIGA supports the following file formats:

Useful or Unusual Features

To one accustomed to MacVector, the first unusual feature is the main Project View window of the project (.PRJ) file, which has been carried over from the previous version. It has three panels: the Tree panel shows a directory tree, in which the files in the project appear as if they were stored in Windows directories - in fact, they can be stored in any directory and are connected only by path names. Results of analyses are stored in files that are linked to their sequence files and can be opened simultaneously in both graphical and spreadsheet windows; the Summary panel displays basic information for each of the highlighted sequences in the Tree panel. The Attributes panel displays formatted data and comments, either user-entered or from the annotations accompanying any of the numerous file formats OMIGA can import.

A very useful addition is the ability to search in and retrieve files from the NCBI database using Entrez and BLAST. The FETCH button imports GenBank flat files, including sequence features and notations, into OMIGA format. There is no need to paste sequences from a browser because there are Database:Retrieve to Disk and Database:Retrieve to Desktop buttons and menu items that allow a user to pull in Entrez and BLAST hits directly. NCBI's formatting of BLAST searches is reproduced by OMIGA: a list and graphical map is displayed, and clicking on a file in either format gets the individual alignment. Dot-plot sequence analysis has also been added to OMIGA. This feature detects regions of sequence similarity between two different sequences (either self or other, DNA or protein), as well as repetitive elements within the same sequence. Regions of similarity are represented as lines in a matrix format; the position is determined by where in each sequence the similarity occurs. The alignments in a region of the matrix can be viewed in the lower panel of the window. "Clouds" of parallel lines near the diagonal indicate local short repetitive motifs, such as ABABAB.

Limitations

The Features View is highly plastic with respect to the individual features that can be simultaneously shown, and the complete list of available features that can be selected individually or in groups is provided in Windows tree format in the adjacent panel. To achieve "publication quality," it would be useful to have more control over the graphical presentation of the features. For example, contiguous adjoining sequence features (represented as "blocks") cannot be lined up along a single dimension but instead are variously offset or "exploded," to provide space to read feature labels. In circular displays, this can lead to large unwieldy figures. Colors are not specifiable - the Features View must be exported as a Windows metafile (.EMF) for further manipulation in a full-featured graphics program.

Motif searches with OMIGA are performed using PROSITE and NASITE, which return an enormous number of hits, and are therefore of questionable utility. In addition, there is no facility to adjust the search stringency. Transcription-factor site searches can be particularly nonproductive, and one such search, of the human IL-2 promoter using eukaryotic regulatory motifs, was no exception. The well-characterized elements NF-AT, NF-kappa b, and NFIL2A were not identified; two AP-1 sites were identified as ATF/CREB sites.

The project file structure can lead to problems. Sequence files borrowed from other projects are not physically copied but rather "inserted" (i.e., linked) and run the risk of being lost if they or the project are moved. Files must first be deleted from the Project View window, and they remain in Windows Explorer until manually deleted from there. Upon opening a project, OMIGA will alert the user about any missing files and search for them. In the event of a system crash, an open project file can be corrupted. This possibility is alluded to in the Getting Started tutorial, in which it is suggested that one make a backup copy of the project. OMIGA can package a project into a single .PAK file, in which the entire project including linked sequence files is copied.

Comparisons with Similar Software

With the addition of Web access, the most frequently used analyses and manipulations performed by OMIGA are comparable to those of MacVector. The structured format of the project environment greatly improves organization and productivity.

Technical Support and Documentation

The documentation is excellent and comprehensive, and includes a main User Guide, tutorials called "Quick Start" and "Getting Started," a Reference Guide detailing the analysis algorithms used, a booklet with the CD detailing installation and registration, and a short photocopied brochure with information on the latest updates and bug workarounds. The user manual is also installed online in PDF format, and there is standard Windows menu-based help. Technical support is available via email, a Web-based form, or by telephone in the United States, England, and Germany.

Target Users

The individual worker in a research laboratory.