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Category: Tips

  • Importing sequences from Addgene into MacVector

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    Chris
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    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…

  • Create constructs using MacVector’s Cloning Clipboard

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    Chris
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    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…

  • Tooltips in MacVector: restriction sites, features and reference assemblies

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    Chris
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    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.

  • 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…

  • The MacVector Team are at the ASM2017 in New Orleans (2-5 June).

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    Chris
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    We’re at ASM Microbe 2017 in New Orleans from Friday until Sunday (2-5 June). The exhibit hall hours are a more respectable 11:30 or 12 until 18:00 now (last year was a quite early 7:30 until the afternoon). We’re on booth #2247. Please do drop by. We’ll be showing our latest release, MacVector 15.5 and…

  • 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…