Major Features
Graphical Sequence Editing
MacVector can read and write DNA and Protein sequences in most popular file formats. In addition to directly editing sequences and features/annotations, MacVector has an intuitive "Click Cloning" graphical interface that lets you easily replicate laboratory cloning experiments to create new molecules. The latest version of MacVector uses the native Mac OS X Quartz graphics to generate publication quality images that can be scaled to any size with no loss of resolution. More details...
Primer Design
You can design primers for either PCR or Sequencing/Hybridization probes using the primer design functions. In addition, you can test specific primers to determine if they have secondary structure problems, alternate binding sites or other characteristics that might impact their use in experiments. More details...
DNA Analysis
MacVector provides a wide variety of useful DNA analysis tools, including base composition analysis, Restriction Enzyme searches, DNA Subsequence searches and "Dot-Plot" comparisons between DNA:DNA and DNA:Protein sequences. A Coding Preference toolbox lets you select a variety of algorithms to graphically scan a DNA sequence for likely protein coding open reading frames. More details...
Protein Analysis
Protein sequences can be reverse translated into DNA, compared using "Dot-Plot" analysis and scanned for Proteolytic cleavage sites and amino acid sequence motifs. A comprehensive Protein Analysis Toolbox provides a wide variety of algorithms for analyzing the composition of proteins and presenting the results in graphical and tabular formats. More details...
Database Searching
MacVector has built-in Internet connectivity to the NCBI BLAST and Entrez databases. You can directly search Entrez for DNA or Protein sequences based on features, authors, keywords etc and directly download them into MacVector, complete with all features and annotations. The built-in BLAST interface lets you submit multiple BLAST jobs using DNA or Protein sequences and then download any matching sequences by selecting them from a hit list. Even without an Internet connection, MacVector can align sequences against any folder on your hard drive using a FastA algorithm, allowing for "local" database searches. More details...
Multiple Sequence Alignment
You can align unlimited numbers of DNA or Protein sequences using the ClustalW algorithm built in to MacVector. A full-featured editor lets you make manual adjustments to the alignments and view them using a wide variety of customizable color schemes. You can create publication quality graphical outputs of the alignments and view pairwise combinations of the sequences in aligned and matrix formats. More details...
Sequence Assembly
Sequence Assembly functionality in MacVector is now provided by two modules. First there is a built-in function called Sequence Confirmation. This is included with MacVector and allows you to import trace files or sequence files and assemble them against a template sequence. This is ideal for small scale sequencing projects, especially resequencing. For example, checking an in situ mutagenesis experiment, a construct you've just made, or confirming the sequence of a cloned PCR fragment. It's also an excellent tool for SNP analysis, with some special tools to allow you to easily spot mutations from your original template sequence.
For full scale sequencing projects where you do not know the sequence you'll need MacVector and a separately purchased plugin called Assembler. This is a full contig assembly application that uses the phred, phrap and cross_match algorithms from the University of Washington to assembles traces into contigs. It displays full quality scores of the reads and the aligned contigs. The trial version of MacVector also includes the Assembler plugin. Click here to go to the Assembler product page.
Please note that AssemblyLIGN is no longer included with MacVector.
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