Overview

MacVector, published by Genetics Computer Group of Madison, Wisconsin, is designed to provide molecular biologists with a tool to analyze nucleic-acid and protein sequences. Version 7.0, reviewed here, represents considerable advancement in terms of features and system requirements over the first release, which ran on a 512K Classic Macintosh and System 6. The package comprises an installation CD, a Getting Started tutorial booklet, a detailed printed manual (User Guide), and an ADB or USB "dongle" that restricts use to properly licensed persons. The User Guide and tutorials are also provided as PDF documents. In addition, online help is also available from a drop-down menu while MacVector is running. A free trial version is available that expires after 30 days although it does not come with printed documentation.

MacVector provides the user with the battery of analytical tools that biologists have begun to demand from their sequence analysis software. The user can analyze single protein or nucleic acid sequences or alignments of multiple sequences. Examples of analytical routines are searching for open reading frames (ORFs), restriction, and proteolytic enzyme sites. Other analytical routines available to the user are construction of phylogenetic trees, gene prediction, mRNA sequence prediction from genomic sequences, and multiple sequence alignments. Sequence property prediction such as the Kyte-Doolittle hydrophobicity plot for proteins and "melting points" for nucleotides are also options. MacVector also allows for integrated BLAST and Entrez searches against databases at the National Center for Biotechnology Information.

The Getting Started tutorial walks a novice through a few simple exercises, such as installing the program, constructing a plasmid, importing sequence files, understanding how to use the Features function, identifying restriction sites, and inserting a coding sequence into the pUC19 vector. I repeated the exercises using a vector of my choice and inserted a cDNA sequence encoding a protein into which I wished to engineer thrombin cleavage sites. I then worked my way through the entire manual testing either vector sequences that came with MacVector, or sequences of my own choice. In most cases, when I encountered roadblocks it was due to making incorrect assumptions or not reading the appropriate section of the manual carefully enough.

MacVector is not overtly intuitive in the way that Macintosh programs can be. However, one has to remember that it delivers a complex set of analytical tools and cannot really be compared to a simple application. Frequent recourse to the manual as each new routine is learned gives the user a feel for MacVector's logic, at which point a certain intuitiveness does become apparent. Overall, my impressions of MacVector were positive, and I would use this program in my work.

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

It soon became obvious that in order to exploit the capabilities of MacVector, I needed to read the accompanying documentation. In less than half an hour, I worked my way through the Getting Started tutorial booklet. At that point I began to get productive. Reading the user guide from beginning to end took longer, approximately a week of daily sessions, each lasting roughly two hours.

Product Quality

Customizability

Not applicable.

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

Not applicable.

Ability to Import and Export in Different File Formats

MacVector can open text files from the following sources: GenBank (flat file format), GenPept, IG Suite, EMBL (flat file format), Swiss-Prot, PHYLIP, NEXUS, Pearson FASTA, GCG (RSF and MSF), ASCII, CODATA, and Staden.

MacVector can write nucleic-acid and protein sequences and alignments as text files for the following destinations: GenBank, GenPept, IG Suite, Swiss-Prot, PHYLIP, NEXUS, FASTA, Staden, GCG (RSF and MSF), NBRF, and ASCII 1-letter (70 residues/line).

Useful or Unusual Features

Limitations

The major weakness I perceived was in the editing options available to modify MacVector's graphic output. While MacVector can draw attractive plasmid maps, modifying them to the user's satisfaction is not easily accomplished. For example, map size changes can be accomplished only by scaling print output. In addition, one cannot specify the position of a map on a page, highlight and delete text, or insert text. I was informed by GCG that this limitation could be overcome by exporting graphic views and editing them in a program that supports rotated anti-aliased text such as FrameMaker.

MacVector can only open sequence files generated from other applications when they are saved as text. Extending its capability to files in proprietary format from other sequence analysis programs would be very useful. Lastly, MacVector is not for everyone, its price restricts users to those with large budgets.

Comparisons with Similar Software

My comparison set was Vector NTI, MacDNAsis, DNA Strider, and GCG on a Unix machine. MacVector occupies a position of strength in this group.

Technical Support and Documentation

The quality of the printed manuals, Getting Started and User Guide, is one of the strengths of this package. The information provided is comprehensive and logically arranged. Additional technical support is available by phone, fax, and email.

Target Users

Molecular Biologists. MacVector can be a valuable desktop aid for the analysis of nucleic-acid and protein sequences and the design and storage of plasmid information.