Tag: annotation
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How to remove gaps from a sequence
There are often times when you end up with a sequence containing gaps, especially if you make extensive use of the Align To Reference, Contig Assembly or Multiple Sequence Alignment interfaces to generate consensus sequences. You can select and copy the consensus sequence, or even individual aligned reads, from the Align To Reference and Contig…
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How to automatically annotate bare sequences
If you have an unannotated vector or other sequence that you’ve been sent from a sequencing lab, downloaded from a web page or been sent by a colleague, it can be very tedious to manually create all the features that you believe are present on the sequence – assuming you even know what is supposed…
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View sequences at the residue level in the Map tab
Many MacVector users do not realize that you can view sequences at the residue level in the Map tab as well as the Editor tab. This has the advantage that you can see restriction enzyme cut sites (including staggered sticky ends) along with the graphical display of features aligned to the residues. You can even…
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Visualising ORF analysis results in the MAP tab.
The Map tab of MacVector is a powerful way to visualise and interact with your sequences. All analysis tools will work directly in the Map tab. You can design primers, ligate and digest fragments from the Cloning Clipboard, visualise translated CDS regions and much more. In fact one of the only tasks, you will need…
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Editing the appearance of individual sequences maps
Although we think that the default appearance of sequence maps in MacVector is very pretty, sometimes the defaults are not to everybody’s taste! If you think this way, then changing how maps look is very easy. Rather than edit the appearance of all of your sequences it is far better to modify the default symbol…
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The “/label” qualifier, features in the Editor tab and MacVector 14.0.2
With MacVector 14.0 we introduced two minor changes that have just not pleased a lot of users. We spend a lot of time discussing all improvements in every release and we did think that these two changes improved MacVector. But a lot of users have complained about both of them. So it looks like we…
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101 things you (maybe) didn’t know about MacVector: #42 – Managing segmented features
If you download eukaryotic genomes from GenBank, you will find that many coding (i.e. CDS) features are segmented and consist of multiple individual segments joined together into a single long feature. You can see an example of this with the human cystic fibrosis transmembrane regulator gene – you find a copy of this in the…
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Importing sequences from ENSEMBL
There’s a few different ways to import annotation from the ENSEMBL database browser, as well as other databases. Using Genbank The easiest way to export from ENSEMBL and keep all annotation is to use the Genbank format. The default format will be FASTA which has no annotation. With Genbank all the annotation is stored in…
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101 things you (maybe) didn’t know about MacVector: #30 – Submitting Sequences To GenBank using Sequin
Note: while preparing this blog post we discovered a bug in MacVector 12.7.4 that prevents submission using the exact steps shown here. Be sure you are using MacVector 12.7.5 or later which has the bug fixed. If you are using an earlier version, send an e-mail to support@macvector.com and we’ll send you the details of…
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101 things you (maybe) didn’t know about MacVector: #26 – Creating Features Automatically
Following on from my recent posts on manual and semi-manual creation of features, the next approach I want to discuss is a fully automated function for creating features. How often do you get sent plain sequences that have no features annotated, even though you know your favorite gene is on there, along with a few…