Sequence Analysis Tools for Molecular Biologists
Overview of Major Features
If you already own an older copy of MacVector, and would like to know what new features have been added since the version you own, you can find that information on this summary page.
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. 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...
Gateway and Topo Cloning
MacVector supports the popular Gateway, TOPO TA and Zero Blunt cloning technologies from Invitrogen. With a few simple clicks from an intuitive graphical interface, you can replicate your biological manipulations at the bench to create new molecules with the correct sequences across the cloning and recombination junctions. More details...
You can scan an unannotated or partially annotated sequence against a folder on your hard drive and MacVector will identify matching features in sequences in the target folder and add them to your sequence. Because MacVector includes custom feature appearance information when annotating the sequence, you can use this to maintain a carefully curated set of your favorite genes and sequences each with a graphical appearance that best suits your needs. More details...
You can design primers for either PCR or Sequencing/Hybridization probes using a variety of primer design functions, including an interactive manual design interface along with several scanning functions such as the popular Primer3 algorithm. The interactive interface clearly shows which potential primers may have secondary structure problems, alternate binding sites or other characteristics that might impact their use in experiments. More details...
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 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...
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 functionality in MacVector is now provided by two modules. First there is a built-in function called Align To Reference. This can be used for two different functions, Sequence Confirmation and cDNA Alignment. 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.