Tag: annotation

  • Importing Genbank files from Safari or other web browsers.

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    Chris
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      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…

  • 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…

  • 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.

  • 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…

  • 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…

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

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    Chris
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    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…

  • Functional domain analysis of protein sequences using InterProScan

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    Chris
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    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…

  • Batch auto annotation of blank sequences with MacVector and AppleScript

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    Chris
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    Over the past few releases we’ve been making more MacVector tools to be scriptable with AppleScript. The latest is Auto Annotation. Auto Annotation is a great tool for curating your sequences. For example if you receive a unannotated sequence then you can scan it against other sequences to find. Blasting an unknown sequence, fetching the…

  • Viewing external database entries for features in a sequence.

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    by

    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 available in MacVector 15). Very useful for when you want to view more detailed or updated information. Within the Genbank specification,…