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!

Tag Archives: annotation

Annotating a gene in MacVector

Creating biologically accurate AND beautiful maps of your plasmids is easy in MacVector. All you need to do is select some sequence, then open the FEATURES EDITOR. Every annotation is fully compatible with the Genbank specification and Feature Table. Tweet

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Controlling Automatic ORF Display

MacVector 15.5 automatically scans every DNA sequence window for open reading frames and displays the results in the Map tab. The setting for this are controlled by the MacVector | Preferences | DNA Map pane, along with the automatic Show restriction sites settings. The Minimum Number of Codons setting is fairly obvious. 5’ ends are […]

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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 […]

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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 […]

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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. Tweet

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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 […]

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Using BLAST to automatically annotate a sequence

You can use the Database->Auto-Annotate Sequence function to quickly annotate a bare sequence using existing annotated sequences on your file system. However, this only works if your collection of sequences contains features representing all parts of the bare sequence. Luckily, if you have an unannotated region after running Auto-Annotate, you can use MacVector’s built-in BLAST […]

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Controlling The Automatic ORF Display in MacVector 15.5

MacVector 15.5 automatically scans every DNA sequence window for open reading frames and displays the results in the Map tab. The setting for this are controlled by the MacVector | Preferences -> DNA Map pane, along with the automatic Show restriction sites settings. The Minimum Number of Codons setting is fairly obvious. 5’ ends are […]

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MacVector 15.5 is out: Graphical BLAST and automatic ORF display.

Our latest release, MacVector 15.5, introduces an entirely new way to view the results of BLAST searches, with an interactive graphical interface that let’s you easily visualize where your query maps to a hit. Unannotated Open Reading Frames are now automatically displayed whenever you open a DNA sequence. A number of changes to the Align […]

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Functional domain analysis of protein sequences using InterProScan

There’s a new tool in MacVector 15 that allows you to do functional domain analysis on your protein sequence using the InterProScan service. InterPro contains multiple databases of protein families, domains and motifs and InterProScan will submit a protein sequence to a search of these databases. It will also do extra analysis such as transmembrane […]

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