MacVector 11.0

MacVector 11.0 is such a professionally designed Macintosh application that supports sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a wide variety of other functions. MacVector is widely regarded as the most intuitive, easy to use program available for sequence analysis.

Major Features:

1. Graphical Sequence Editing
   • File Formats: By default, MacVector reads and writes files in its own binary format in order to preserve as much information as possible about a sequence. However, the program can also read and write files in the following sequence formats: GenBank/GenPept, EMBL/SwissProt, Staden, IGSuite
   • Sequence Editing
   • Sequences can be edited using the fully functional Sequence Editor. As well as ensuring that feature locations are correctly maintained during edits, an audio function lets you playback selected residues for easy proofreading. Toolbar buttons let you view and edit the features, annotations and graphics associated with each sequence.
   • The sequence editor also acts as the primary window from which you can launch all MacVector analyses. All functions are integrated into a single MacVector application- no need to switch to a different module or program to find the algorithm you are looking for.
   • Feature and Annotations Editing: Interactive lists of features and annotations can be viewed by clicking on a particular tab. MacVector considers features to be those annotations that have an actual location on the sequence. All other attributes (e.g. literature references or keywords) are considered to be an annotation. MacVector supports the full list of GenBank keywords and qualifiers. Creating a new feature is simple - just select the region of interest in the editor window, then click on the "+" button in the feature list window.
   • Graphical Features View
   • One of the strengths of MacVector is the ease with which high quality detailed graphical views of a sequence can be generated and copied into other compatible applications. The latest versions of MacVector have enhanced this further by using OS X "Quartz" graphics and text for all of the Feature Graphics.
   • Clicking on the graphic button on the sequence window toolbar opens up the the interactive feature graphic window. You can turn on and off the features you want displayed and control all aspects of their appearance such as shape, color, pattern, fonts, position, size etc. Sequences can be viewed in linear or in circular format (great for plasmid constructs). When a feature object is selected, this also selects the corresponding region in the sequence editor and feature list view, greatly simplifying the selection of regions for copying or additional analyses.
   • Double-clicking on a feature opens up a symbol editor allowing you to change the appearance of individual or groups of features.
   • The graphics are drawn using "Quartz", the native imaging system of Mac OS X. This means that the objects retain their high resolution at any scaling and can be printed at extremely high quality with non of the "jaggies" associated with bitmapped graphics. In addition, the graphics can be copied and pasted into any application that supports PDF graphics. On the Macintosh, this includes the Apple applications Preview, TextEdit, Pages and KeyNote. Microsoft Office 2008 also supports this, although Office 2004 does NOT support PDF-based pasting.
   • "Click Cloning": Many of MacVector's analysis functions generate graphical result windows similar to the feature graphic view. In particular, you can use the Restriction Enzyme result window to replicate laboratory cloning experiments in silico. You can click on a restriction enzyme site, hold down the key and then click on a second site to select both sites along with the intervening DNA. When the selection is copied , the DNA sequence, enclosed features, graphical appearance information and the structure of the ends are all placed on the clipboard. You can then move to a second graphical result window, select compatible target sites and paste in the copied DNA to create a new recombinant molecule. MacVector will "flip" copied molecules if required to match the target sites and will refuse to paste incompatible ends (although you can choose to override this if you wish). The main feature window also has a dynamic Restriction Enzyme function that makes this easier to do
2. Primer Design
   • Searching for PCR primers: You can use MacVector to identify pairs of primers suitable for use in Polymerase Chain Reaction experiments. You can choose to a region of a sequence that you wish to amplify, or simply ask for a product within a certain size range. The primers are selected based on similar criteria to the sequencing primers, except that the default reaction conditions are adjusted to reflect the high primer concentrations used in PCR experiments. In addition, MacVector ensures that pairs of primers will not interact with each other, or with the predicted amplified product. MacVector can also design internal hybridization primers for use with realtime PCR analyses. You can either design primers in as few as three mouse clicks, or alternatively fine tune te design using the advanced options.
   • Searching for Sequencing Primers/Hybridization Probes
   • You can use MacVector to identify suitable primers to use in sequencing reactions or as hybridization probes. In its simplest form, you simply define the approximate region of the DNA and the strand where the probe should bind and MacVector will generate a list of suitable primers.
   • In general, you need to find a primer that will not hybridize to itself, shows no internal secondary structure, will bind to a unique site on the target DNA, and has reasonable length and binding characteristics. MacVector provides well defined defaults for all of these, but lets you change any of the individual parameters for greater sensitivity.The results are presented in both a textual and graphical format. The text format lists the binding site location, sequence, %G+C and Tm of each suitable primer while the graphical view displays the locations of the primers relative to the rest of the sequence.
   • Testing Sequencing Primers/Hybridization Probes: If you are performing mutagenesis experiments or other investigations where you have a defined primer you wish to use, you can use MacVector to determine the binding characteristics of the primer. Simply type/paste the sequence of the primer into the "Test Primer" dialog and you can get instant feedback of any potential problems.
3. DNA Analysis
   • Base Composition Analysis: MacVector lets you plot and/or list a wide variety of base composition statistics, all driven from a single easy to use dialog. You can list the total mono-, di- and tri-nucleotide frequencies within a selected segment of DNA and plot the occurrence of individual di- or tri-nucleotides (e.g. CpG dinucleotides) as histograms. You can also plot base composition across a DNA segment, combine plots onto a single graph and zoom in to view regions of interest in more detail. You can also plot and list melting temperature statistics under a variety of experimental conditions.
   • Restriction Enzyme Searches: MacVector can search DNA sequences for restriction sites using any or all of the enzymes from the REBASE Restriction Enzyme Database. It maintains lists of enzymes in individual files representing not only all of the enzymes in the database, but also broken out my manufacturer. You can duplicate and/or edit these files to create your own custom lists of enzymes or even add new specificities. You can also select individual enzymes within each file to allow fine control over the enzymes used in a search.
   • When you perform a search, you can not only choose the enzyme file you want to use, but you can also choose how you want the search to be performed - you can simply search using all enzymes in the file, or just the selected enzymes, or you can choose combinations of other criteria such as site size, end structure or number of cuts in the molecule. Once the scan has completed, you can apply additional post-processing filtering to help identify cut sites of interest and what information you would like to display.
   • The predicted cut sites can be listed in a variety of ways and displayed on an text-based annotated sequence as well as an interactive graphical map of the sequence. You can also choose to display all of the enzymes that do not cut the selected DNA segment and lists of the fragments that would be produced by all combinations of single and double digests.
   • DNA Subsequence Searches: MacVector can search for DNA subsequences using a very similar approach to the Restriction Enzyme searching functionality. However, you can use subsequences with complex patterns for the search - each pattern can have up to three distinct segments, separated by variable inter-segment regions, and you can control the overall similarity required for a match as well as defining residues which must be 100% conserved. MacVector ships with a number of collections of interesting sites, including the popular tfsites Transcription Factor database
   • Dot Plot Sequence Comparisons: You can use Dot-plot comparisons to identify weak relationships between sequences or to identify repeat sequences. MacVector lets you not only compare pairs of DNA sequences, but also a DNA sequence with a protein sequence. The output can be viewed graphically and also as a text view where the segments of similarity from the second sequence are displayed aligned underneath the annotated first sequence
   • Coding Preference Toolbox: MacVector bundles a number of algorithms useful for identifying protein coding open reading frames into a single Coding Preference Toolbox. It includes a simple algorithm for displaying open reading frames longer than a specified number of residues in addition to plots of codon-specific G+C%, Fickett's testcode, Uneven Positional Base Frequencies, Positional Base Preference and three Codon Preference algorithms (MacVector, Staden and Gribskov) that plot coding probability using pre-calculated organism-specific codon usage tables. The results of each algorithm are displayed on an interactive graphical display that lets you zoom in all the way to the residue level if required and lets you select potential open reading frames to translate by clicking on start codons or on entire open reading frames.
4. Protein Analysis: MacVector provides a wide range of tools for analyzing Protein sequences. In addition to the single sequence analyses present below, you can also align multiple proteins using ClustalW and scan databases for related proteins over the Internet or locally on your own file system.
   • Protein Analysis Toolbox: MacVector provides a variety of algorithms that you can use to analyze the composition of protein sequences. These range from simple composition reports (counts of each amino acid, pI and molecular weight) to hydrophobicity, antigenicity and secondary structure predictions. All are accessed through a single Protein Profile Analysis dialog.
   • The results can be viewed graphically using filled plots so that you can see at a glance if a protein is above or below the average for the displayed analysis. As with the DNA coding preference plots, you can zoom in to the residue level to closely examine interesting regions.
   • Proteolytic Enzyme Searches: MacVector lets you scan a protein sequence for proteolytic enzyme cleavage sites in a similar way to searching DNA sequences for restriction sites. MacVector provides a reference file containing all of the currently known useful proteolytic enzymes and you can add your own using the built-in editor. The results can be viewed in text or graphical format, with similar filtering options to those available for restriction enzyme searches.
   • Amino Acid Motif Searches: MacVector can search for Amino Acid subsequences using a very similar approach to the Proteolytic Enzyme searching functionality. However, you can use subsequences with complex patterns for the search - each pattern can have up to three distinct segments, separated by variable inter-segment regions, and you can control the overall similarity required for a match as well as defining residues which must be 100% conserved. MacVector ships with a number of default amino acid subsequence files derived from the popular PROSITE database.
   • Reverse Translation: You can reverse translate a protein into its equivalent degenerate DNA sequence using the translation code of your choosing. In addition to creating the corresponding DNA sequence, MacVector can also scan the sequence for the least degenerate nucleotide sequences than can be used as probes or PCR primers to identify those sequences in a genomic library.
   • Dot-Plot Analysis: Pairs of protein sequences can be scanned for sequence similarity to each other using the Dot-Plot functionality, in a similar way to DNA sequences. However, you can also compare a protein sequence to a DNA sequence to identify weak relationships between a protein sequence and a related protein-encoding DNA sequence.
5. Database Searching
   • NCBI Entrez: The National Center for Biotechnology Information (NCBI) maintains a number of sequence databases that can be accessed over the Internet. MacVector has a built-in Internet database browser that lets you search the NCBI's Entrez databases for sequences using combinations of search terms such as author, organism, keywords, accession number etc.
   • Sequences that match the search terms can be downloaded either individually or in batches to your desktop or to a folder on your hard drive. Sequences are retrieved with all of their associated annotations and features intact. These can be viewed and edited in MacVector, or used for additional analyses.
   • NCBI BLAST: The Basic Local Alignment Search Tool (BLAST) algorithm is a popular program for identifying sequences in a databases that share sequence similarity to a search sequence. MacVector provides an integrated Internet BLAST interface to the databases at the NCBI. You can search using any of the blastn, blastp, tblastn, blastx and tblastx algorithms using any sequence databases available at the NCBI. The BLAST searches take place in the background, so you can continue to work with MacVector while one or more searches are in progress. As well as providing a standard BLAST report of the best aligning sequences in the database, MacVector also lets you select sequence in the "hitlist" and directly download those to your desktop or hard drive for further analysis.
   • Align To Folder
   • As well as providing database searches over the Internet, MacVector has a built-in sequence searching facility that you can use to find similarities in collections of sequences stored on your own hard drive. The search algorithm is based on the popular FastA programs - you simply select a folder containing a collection of sequences and MacVector will scan through every sequence file in the folder looking for similarities. For this search, MacVector can use not only FastA formatted sequences, but also sequences in MacVector format, any chromatogram file format, and a number of simple text based formats.
   • As well as displaying a list of matching sequences and a graphical overview of the alignments, the Align to Folder function also generates a detailed text alignment showing each matching sequence aligned with the annotated search sequence. This is particularly useful for identifying the locations of sequence differences in relation to protein coding regions or other features on the search sequence.
6. Multiple Sequence Alignment: You can use MacVector to align related DNA or Protein sequences. MacVector uses the ClustalW algorithm to automatically align any number of sequences and provides a sophisticated editor that lets you fine tune the alignments. The alignments can be output in a variety of formats or used to generate phylogenetic reconstructions using a number of built-in algorithms.
   • Creating Alignments: You can create alignments from sequence already open in MacVector, or by creating an empty alignment and populating it with sequences imported from disk. You can also directly open an existing file containing multiple sequences. MacVector supports the following multiple sequence file formats
   • Automatic Alignments: MacVector uses the ClustalW algorithm to align both DNA and Protein sequences. ClustalW 1.83 is used and alignments are submitted into the Job Manager to run in the background, allowing you to continue to work with MacVector.
   • Editing: The MSA editor provides full editing facilities, including inserting new residues or even adding new sequences from the clipboard. You can change the order of the sequences, copy regions of the alignment to other windows and slide selections around on the screen. The consensus sequence is always updated dynamically and you can control how the consensus is calculated.
   • Output Options: The aligned sequences can be displayed in result windows in a variety of different ways. One window provides a high quality customisable graphical text display designed for output on a laser printer, while another duplicates the output from ClustalW. You can also view the sequences aligned in pairwise mode, along with a matrix displaying the identities and similarities of each pair of sequences.
   • Phylogenetic Reconstruction
   • You can use MacVector to generate phylogenetic reconstructions from a multiple sequence alignment. Clicking on the "create tree" icon in the multiple sequence alignment editor brings up a phylogenetic reconstruction dialog where you can choose the algorithm and distance correction methods to use. MacVector supports two main reconstruction algorithms - Neighbor Joining and UPGMA, that can be used with Best Tree or Bootstrap calculation modes. A variety of distance correction and gap treatment parameters allow further refinement of the algorithms.
   • The reconstructed phylogeny is viewed in a graphical window where you can control the type of tree displayed (phylogram or slanted or regular cladogram), the node used for rooting and a variety of other display characteristics.
7. 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.

Enhancements:

• 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.
• Click Cloning Enhancements: 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.
• 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.
• 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.
• 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.
• Miscellaneous Enhancements: As always, we 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
• Availability: MacVector 11 is available now!

Requirements:

• Operating System
• • MacVector requires Mac OS X 10.4 or above. MacVector does not run on Mac OS 9 ("Classic") or on Microsoft Windows based "PC" computers.
  • It's recommeded that the use of Mac OS X 10.5 or later for the most complete graphical functionality and highest quality images.
• Hardware
• • Any Macintosh computer capable of running Mac OS X 10.4 or later is sufficient to run MacVector. MacVector runs natively on both PowerPC and Intel-based Macintosh machines.