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 FastA GCG SSF GCG MSF GCG RSF NBRF BSML ASCII ABI SCF DNAStrider GeneWorks Phylip Nexus |
Read y y y y y y y y y y y y y y y y y |
Write y y y y y n n y y y y n y n n y y |
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.
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 version of MacVector has 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.
Interactive lists of features and annotations can be viewed by clicking on a toolbar button. 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.
"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 <shift> 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).
A floating palette window lets you quickly adjust the visibility of features, either in groups or individually. The palette also controls additional functions such as page layout, shadow, anti-aliasing etc.
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. The current version of PowerPoint for the Macintosh does NOT support PDF-based pasting. Graphics must be imported into PowerPoint using bitmapped images which reduces the quality of circular arcs and rotated text.
