The Macintosh has long been molecular biologists' computer platform of choice. In reward for their loyalty, these biologists have had an excellent selection of professional DNA analysis software available only for the Macintosh. MacVector 6.0 by Oxford Molecular Group is a good example of such a program. Oxford Molecular Group, which acquired MacVector from Eastman Kodak last year, has incorporated significant improvements into version 6.0. The most notable improvements include Integrated Internet access and multiple sequence-alignment functions. MacVector is a small program, requiring only 8 Mb of hard drive space, but the small size belies its power and versatility. MacVector provides a beautifully streamlined and efficient interface for performing the everyday editing and analysis of DNA sequence data.

Figure 1

MacVector offers a straightforward sequence editing interface (see figure 1), which allows standard manipulation of DNA sequences. Sequence data can be entered manually, imported from a text file, or obtained directly from an IBI gel reader. Insertion, deletion, cutting, and pasting of DNA sequences can be performed in the editing window. Functions for reverse, complement, and reverse complement of sequence data are available. A digitized voice can be used to proofread a sequence during or after data entry. A MacVector sequence file can store valuable annotations such as literature references, keywords, or a description of the sequence. Features of DNA or protein sequences such as promoters, open reading frames (ORFs), or disulfide bonds can also be recorded and saved in a MacVector data file, conveniently storing large amounts of information about a specific sequence of interest.

Figure 2

Once the DNA sequence has been entered, a variety of data analysis functions are available. Restriction maps can be created in standard table formats or in a graphical representation (see figure 2). These maps can be fully configured by the user. The graphical maps generated by MacVector are useful for reference purposes, but are not of publication quality. Nucleotide sequences can be searched for ORFs, and can be translated into the corresponding amino acid sequence. DNA sequences can also be searched for conserved sequences or specific motifs such as transcription factor binding sites. The DNA subsequence database can also be edited by the user as needed.

Figure 3

MacVector can perform alignments of up to 30 DNA or protein sequences using the Clustal W algorithm. All alignment parameters are user configurable, and the output of the multiple sequence alignment can be saved as high-resolution PICT files for use in publications (see figure 3). Pustell protein and DNA matrix functions are also available.

Figure 4

In addition to DNA sequence analysis, MacVector can perform an array of analysis on a given protein sequence. Simple structural features such as alpha helices, beta regions, and turn regions can be predicted using the Chou-Fasman or Robson-Garnier methods. Searches can also be made for known protease digestion sites within the primary protein sequence. Theoretical calculations for hydrophobicity, hydrophilicity, surface probability, flexibility, pI, and antigenicity are all available in the protein analysis toolbox and can be presented graphically (see figure 4). MacVector also provides functions to search a polypeptide sequence for protein subsequences from a user-edited database.

MacVector can search a DNA sequence or template for potential PCR primer pairs. The program selects primers with maximum specificity for the region to be amplified, and eliminates primers that can form secondary structures or primer dimers. Degenerate oligonucleotides can also be designed from a given protein sequence.

Figure 5

MacVector's most impressive feature is the seamless manner in which Internet database searches have been integrated into the program (see figure 5). Internet searches are performed via the NCBI Web site. Once a sequence of interest has been retrieved it can be browsed, or sent directly into the sequence editor for analysis. BLAST searches can be performed instantly on sequences in the DNA editor window. Internet searches using MacVector were surprisingly quick and noticeably faster than those using a conventional Internet browser. The Internet browser window can also be used for MEDLINE searches of the literature. If desired, database searches may be performed locally using NCBI sequence database CD-ROMs, but these do not always contain the latest sequences entered in the database.

Unfortunately, MacVector 6.0 has a few limitations that make it less than ideal for all laboratories. One is that the only commercial device that is compatible with the software is the IBI gel reader. The ability to interface with a gel reader allows the analysis of digitized sequencing gels or restriction digests. In addition, the software does not accept data or read chromatogram files from automated sequencers. These minor shortcomings make MacVector less than ideal for labs performing large-scale sequencing projects. In addition, MacVector cannot piece together contiguous DNA sequences. Fortunately, Oxford Molecular Group ships a separate program with MacVector, Assembly LIGN, for those requiring this feature.

MacVector takes full advantage of the Macintosh user interface and creates a sleek environment for the manipulation of DNA and protein sequence data. With just a click of the mouse, users can move effortlessly from sequence editing to BLAST searches to restriction analysis. The combination of innovative Internet connectivity with a highly efficient user interface makes MacVector one of the best-designed software packages for standard DNA sequence analysis for the molecular biology laboratory.

MacVector is available only for the Macintosh and will run on any 68000 or Power Macintosh processor except the Macintosh Plus and earlier models. System 7.0 or a later operating system is required, and 8 Mb of RAM is recommended for running the software.

Oxford Molecular Group can be called in the United States at (800) 876-9994 and in the United Kingdom at +44 1865 784600, or by fax at (408) 879-6302. Their American and British Web sites offer a downloadable demo version of MacVector 6.0, and additional contact information including worldwide distributors.