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#MACVECTOR PLASMID MAPPING HOW TO#
#MACVECTOR PLASMID MAPPING WINDOWS#

Melissa Caimano on HOW DO I video guides to common molecular biology workflows.admin on HOW DO I video guides to common molecular biology workflows.mariam abdelmalak on Major release details – Summary.Brian on Designing primers and documenting In-Fusion Cloning with MacVector.Chris on Designing primers and documenting In-Fusion Cloning with MacVector.Simulating DNA electrophoresis in agarose gels using MacVector’s Agarose Gel tool.

#MACVECTOR PLASMID MAPPING HOW TO#

MacVectorTip: How to copy a specific short amino acid translation of a sequence.

MacVectorTip: Trimming trace files by quality.

MacVectorTip: Identifying, Selecting and Assembling NGS reads with a variant genotype.

To this end, you will also see that the Topology button has now been added to the default toolbar button set of all the sequence window tabs to help indicate it is an important property of the sequence. However, we plan on adding much better support for circular sequences in MacVector 11.5, so we thought it important to clean up this ambiguous linear/circular issue in this release. Displaying misleading results is something that we definitely do not want to do!Ĭurrently, only the restriction enzyme, subsequence searching and (most) nucleic acid toolbox plots consider linearity/circularity in their algorithms. It’s a fairly small change, but unfortunately it has confused quite a few users! We do think that it is safer to have made this change. So now whenever you view a linear sequence the floating graphics palette linear/circular button is disabled to prevent you from inadvertently changing the Map and *thinking* you are dealing with a circular molecule. the aforementioned example of viewing the MCS of a plasmid. We could not think of any user need for viewing a linear sequence as circular, although there are many advantages for viewing a circular sequence as linear. We thought that it was safer to change this behaviour in MacVector 11, and so now although you can view a circular molecule as linear, you cannot view a linear molecule as a circular one. That’s going to produce a confusing set of fragments on a gel! Prior to MacVector 11 if you now viewed this as a circular plasmid the restriction site is still absent, yet the molecule appears to be circular. However, if you have toggled the topology button in the sequence window, the sequence is now linear and the Eco R I site disappears. As a plasmid the sequence’s topology should be circular. A classic example is the cloning vector pBR322, which has an Eco RI site that crosses the origin. Thus meaning that some algorithms would provide unexpected results.

#MACVECTOR PLASMID MAPPING WINDOWS#

However with the new unified tabbed windows viewing a circular view of a linear sequence gives the incorrect impression that you are viewing a circular sequence. This made complete sense with the old sequence model of MacVector. There are times when it is nice to display a circular sequence in linear mode – when you want to zoom in on a crowded region for example, or looking at the MCS of a plasmid whilst cloning fragments. This button has always been a visual function, and it does not affect the real topology of the sequence underneath. One such function is the linear/circular button in the floating graphics palette. However, this major change has left quite a few legacy functions that do not fit the new model so well. This is great for visualising your sequences. For example with three replicas open, one showing the sequence, another the feature table and the third the map view, then if you select a gene feature in the Feature table, then the sequence representing that gene will be highlighted, and the feature in the Map window will also be highlighted. Furthermore because of this single sequence model all windows are linked, and you can view multiple windows (we call them replicas) of that same sequence. With this more flexible approach regardless of which view you are looking at, or modifying, you are acting on the sequence directly. In MacVector 10 this changed to a tabbed window with multiple dynamic views representing the same sequence model underneath. The actual sequence was only represented in the editor. Prior to this release single sequences were displayed in the sequence editor with static views of the graphical map and feature table available from this single window. One of the major changes was in MacVector 10. We have made some fairly radical changes to the interface over the last few years, and inevitably there are some changes that you know will confuse long time users but are needed to make the interface more consistent and logical. With each new release of MacVector we have always strived to be the easiest to use sequence analysis application.