MacVector 11.0.1

Major Features:

1. 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...
   
2. 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...
   
3. 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...
   
4. 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...
   
5. 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...
   
6. 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...
   
7. Sequence Assembly
   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.
   

Enhancements:

1. Auto Annotation.
   How often have you received or downloaded a vector or other DNA sequence that has no annotations? The new auto annotation function in MacVector 11 can scan a folder full of existing annotated sequences and automatically add matching features to the bare sequence. Not only does the algorithm add the features, but it also copies the appearance information of the matching features so you can be assured that e.g. an ampicillin resistance gene is always a blue arrow, an M13 origin is always a striped red box etc.
   In MacVector 11 you can manipulate the ends of restriction fragments before joining them together. A new interface lets you cut back or fill in each end of the source or target molecule before ligation
   
2. Floating Analysis Toolbar.
   For those users who prefer to click on toolbar buttons to initiate analyses, MacVector 11 introduces a new floating toolbar window containing buttons for all common MacVector analysis functions. You can customize the toolbar to show just the functions you use most often or show them all for rapid access to every available algorithm. You can also add analysis buttons to the toolbars of normal sequence windows for ready access to commonly used functions.
   
3. Sequence Editor Changes
   The primary sequence editor has been rewritten using modern OS X code to better handle long sequences and to provide an OS X look and feel. In addition, you can now display 3 or 6 frame translations below the sequence that update instantly as you edit the sequence.
   
4. Next Generation Sequencing
   The optional add-on assembler module has been enhanced to provide support for next generation sequencing machines. Short read data may be imported in Fastq format and assembled them using the latest version of phrap.
   
5. Miscellaneous Enhancements.
   As always, you add a slew of minor enhancements to each release of MacVector designed to improve workflows, speed up processing or provide better integration with the operating system. Look for the ability to change the colors of chromatogram file displays for red/green color blind users, improved import of sequences from Vector NTI and better handling of genomic sequences.