Tag: weeklytip

  • How to toggle between 1 and 3 letter amino acid codes

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    Chris
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    MacVector displays amino acid translations in many different result windows. You can drill down to the residue level in the Map tab and see translations of CDS and other translatable features and see translations in the plain text views and the Quicktest Primer interface. The translations can be viewed as either single letter codes or…

  • MacVector’s compatibility with different versions of macOS/OS X

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    Chris
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    We strive to ensure MacVector has good forwards and backwards compatibility. For example, MacVector 15.1 will still open files created with the very first version of MacVector! However, since Apple releases a new operating system every year, and generally make fairly significant “under the hood” changes, it is just not possible to support every version…

  • Clone construction using Digest/Ligate rather than Copy/Paste

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    Chris
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    We’ve previously looked at using Edit | Copy and Edit | Paste to quickly and simply create new constructs using Restriction Enzyme sites. Here’s an alternative approach, using the Digest and Ligate buttons and the Cloning Clipboard. The sequence window Map tab has two buttons called Digest and Ligate. These work in a very similar…

  • Viewing external database entries for features in a sequence.

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    Chris
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    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,…

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

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    Chris
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    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…

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

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    Chris
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    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…

  • Using BLAST to automatically annotate a sequence

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    Chris
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    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…

  • Use the BLAST Map to better identify blast hits

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    Chris
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    With the advent of cheap Next Generation Sequencing technologies, there has been an explosion of whole genome sequences deposited in BLAST databases. One consequence of this is that, particularly for sequences of bacterial origin, most of the significant hits are to entire genomes. The classic BLAST results show the sequence alignments, but give no indication…

  • Controlling The Automatic ORF Display in MacVector 15.5

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    Chris
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    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…

  • Clone construction using Digest/Ligate rather than Copy/Paste

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    by

    Chris
    in

    In previous post we looked at using Edit | Copy and Edit | Paste to quickly and simply create new constructs using Restriction Enzyme sites. This post will look at an alternative approach, using the Digest and Ligate buttons and the Cloning Clipboard. The sequence window Map tab has two buttons called Digest and Ligate.…