General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Importing Genbank files from Safari or other web browsers.

 

While MacVector does have a built-in Entrez browser (Database | Internet Entrez Search) you can easily import GenBank formatted text into MacVector via a simple copy and paste approach. Many sequence-oriented web sites have the option of viewing sequences in GenBank format. This format always starts with the text LOCUS and finishes with two forward slashes (//). Simply select starting at LOCUS, hold down the [shift] key and scroll down the document until you see the // at the end and complete the selection to that point as shown below. Choose Edit | Copy to copy the entire text. Now switch to MacVector and choose File | New From Clipboard. This will create a new window containing the fully annotated sequence.

Genbank is a fully open and universally supported sequence format and supports ALL biological annotation and features contained in a sequence. Genbank is the format used by the NCBI, EMBL and DDBJ. It’s updated yearly and ensures that any sequence is viewable by any researcher worldwide, regardless of the software they are using.

MacVector is fully committed to being open about sequences and ensuring researchers can always exchange sequences without being locked into a proprietary format. We always fully support the import and export of Genbank sequences and we always update MacVector to be fully compatible with the Genbank format.

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Importing sequences from Addgene into MacVector

The Addgene repository is a great place for obtaining expression vectors and other plasmids for your research. Fully annotated sequences are available for most plasmid sequences, although older plasmid deposits may be only partially annotated. All are very easy to import into MacVector.

All Addgene sequence deposits have a Genbank formatted sequence. This should contain the annotated sequence available for the plasmid entry. There is no advantage at all in downloading the sequence in any other format.

Just download the Genbank file and double click to open it in MacVector. MacVector will parse all annotation and present you with a full graphical map of your sequence. As long as the Genbank file is correct, this should be identical to the plasmid map on the web page.

You can also copy a sequence from a browser and go to FILE | NEW FROM CLIPBOARD.. to automatically import.

Addgene

Don’t forget that if you are using MacVector 15.5 or later then you will also see automatically annotated restriction enzymes and open reading frames.

Genbank is a fully open and universally supported sequence format and supports ALL biological annotation and features contained in a sequence. Genbank is the format used by the NCBI, EMBL and DDBJ. It’s updated yearly and ensures that any sequence is viewable by any researcher worldwide, regardless of the software they are using.

MacVector is fully committed to being open with sequence data and ensuring researchers can always exchange sequences without being locked into a proprietary format. We always fully support the import and export of Genbank sequences and we always update each new release of MacVector to be fully compatible with the Genbank format.

(August 2, 2017 edited with a few corrections from Addgene via Twitter! Thanks!).

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Simple but accurate restriction enzyme based clone construction using Copy and Paste

The quickest and simplest way to create restriction enzyme generated constructs in MacVector is to use Edit | Copy and Edit | Paste. The strategy to use is identical to copying a paragraph from one Microsoft Word document to insert into a second document. i.e.

Select the restriction enzymes flanking the source fragment in either the Map tab of the sequence window, or the Map Results tab after a Restriction Enzyme analysis. Hold down the [SHIFT] key to select the second enzyme. In circular maps, the selection always proceeds in a clockwise direction, so the order you select is important.
Choose Edit | Copy. This places the fragment onto the system clipboard, along with sticky end information.
Switch to the destination vector. Select the target restriction enzyme site(s). When selecting two sites, make sure you select the fragment you want to replace.
Choose Edit | Paste. If the restriction enzyme site(s) have ends compatible with the copied fragment, this will insert the fragment from the system clipboard into the vector. If the ends are incompatible, you will get a warning “ligation dialog” with options to fill or cut back ends to make them compatible.

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Create constructs using MacVector’s Cloning Clipboard

You can create new constructs in MacVector by selecting two restriction enzyme sites, choosing Edit -> Copy, selecting a target restriction site in a different molecule and then choosing Edit -> Paste. It works great and fully understands compatible overhanging sticky ends preventing you from accidentally creating biologically impossible molecules. However, a far more flexible approach is to use the Cloning Clipboard. Select the restriction sites at the ends of your source molecule in the Map tab (hold down to select the second site), then click on the Digest toolbar button (or choose Edit -> Digest) and the fragment will be placed onto MacVector’s Cloning Clipboard. You can then join fragments together by simply clicking on an end and dragging it onto the end of a different fragment.

Again, MacVector understands that the ends need to be compatible before they can be joined and even allows you to fill or cut back ends to make them compatible. You can join one end of a single molecule to the other to create a new circular molecule, or click on the Circularize button. You can also use this approach to create complex multi-step molecules generated by Gateway or Gibson cloning technologies.

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Tooltips in MacVector: restriction sites, features and reference assemblies

Every aspect of MacVector is designed to help you visualise and see information about your sequence and its annotation. Most views have tooltips that display information about restrictions sites, genes, CDS, SNPs, INDELS and much more.

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Viewing external database entries for features in a sequence.

Sequences, or regions of sequences, can be linked to external databases. For example an entire sequence entry or for when annotation tools are used to annotate proteins with domain or motif information (e.g. InterProScan). Very useful for when you want to view more detailed or updated information. Within the Genbank specification, which MacVector extensively uses, an external database entry can be stored in a /DB_XREF qualifier. This allows the database entry to be easily viewed. The Genbank (and Genpept) specification allow for many different databases to be accessed using this qualifier.

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In MacVector the original database entry can easily be viewed in a web browser by selecting, then right clicking the feature entry in the Features tab and viewing the available DB_XREF entries. Selecting one will load it in your web browser.

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Tear-off Result Window Tabs: make viewing results easier.

All analysis results for an individual sequence are collected into a single tabbed result window to reduce window clutter. However, there are times when it is very convenient to have results displayed in side-by-side windows. For example, if you run a dot plot you can zoom in to view sections of the comparison by drag-selecting over a region of interest in the Matrix Plot tab and the Aligned Sequence tab will update to only display the text alignments across the new selection. Constantly toggling between the tabs to drill down to the region you are interested in (e.g. a potential splice site on a genome versus cDNA alignment) can be very frustrating.

All you need to do is to click on the title of a tab, hold down the mouse button, then drag the selected tab away from the parent window. When you let go of the mouse button, a new window will be created containing just that single tab.

NewImageNot only that, you can organize the tabs into multiple windows if you like. If you drag a tab from one window and drop it onto the tab bar of another window (this only works on the tab bar, you can’t drop on the content region of a window), then the tab will be added to the target window.

Give it a try and get your result windows under control!

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MacVector 15.5.3

There’s another update available with a few minor bug fixes. Update by going to MACVECTOR > CHECK FOR UPDATES

The changes in MacVector 15.5.3 are described in the Release Notes . You can also read more about the new features in MacVector 15.5 on our What’s New In MacVector 15.5 page.

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MacVector for Windows update: Using the Cloning Clipboard.

Macvector for Windows is getting closer.

Here’s a short screencast on using the Cloning Clipboard:

 

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Use the Edit | Transformations menu to change the case of sequence residues

Sometimes it is useful to use a mixture of cases in a sequence. You might want to flag an interesting region and have it easily identifiable in other views. You can change the case of a selected region of a sequence in MacVector using the Edit | Transformations menu.

The case is maintained in all of the related MacVector sequence display windows. In particular, the plain text output windows from all of the analysis functions honor upper/lower case so you can easily identify results surrounding your region of interest.

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