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Tag: annotation

  • Importing SnapGene files into MacVector

    Importing SnapGene files into MacVector

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    Chris
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    MacVector will directly import SnapGene DNA files. You just need to use FILE | OPEN or double click the file. This is very useful when downloading plasmid sequences from the wonderful Addgene plasmid repository. Here’s a plasmid sequence downloaded from the Addgene website in Snapgene format. It’s been opened directly in MacVector by double clicking…

  • Applescript: batch translation of CDS features

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    Chris
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    Apple’s AppleScript (along with Javascript for Automation) is an easy to write and easy to understand language that allows you to easily automate tasks in supported applications. Many Apple applications have a AppleScript Dictionary that defines what functions you can automate. MacVector has many such functions in its AppleScript Dictionary. You can auto annotate multiple…

  • MacVector 18.1 and the new InterProScan functional domain analysis tool

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    Chris
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    MacVector 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 region analysis using TMHMM and other tools.MacVector…

  • Make more of your alignments with MacVector 17.5

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    Chris
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    Our latest release MacVector 17.5 gives you new tools to make the most of your alignments. It displays shared domains in protein alignments to visualize the relationships between aligned proteins. It introduces Flye for de novo assembly of PacBio and Oxford Nanopore long reads and a slew of enhancements to the Contig and Align to…

  • Use Database | Auto-Annotate Sequence to annotate prokaryotic genomes

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    Chris
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    The continuing advances in Next Generation Sequencing have made it relatively low cost to sequence prokaryotic genomes. Many scientists are embarking on large projects to sequence multiple related genomes. These might be clinical isolates of the same species exhibiting different pathogenetic properties, environmental isolates from different sites, or a study over time of the changes…

  • Scan For… Missing Primers: Automatic Primer Binding Site Display

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    Chris
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    One new feature in our MacVector 17 release is the ability to automatically display primer binding sites in each DNA sequence that you open. Here’s an example of a couple of primers displayed on the popular pET 47b LIC cloning vector on each side of the LIC cloning site. The image shows how MacVector 17…

  • Use Database | Auto-Annotate Sequence to annotate prokaryotic genomes

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    by

    Chris
    in ,

    The continuing advances in Next Generation Sequencing have made it relatively low cost to sequence prokaryotic genomes. Many scientists are embarking on large projects to sequence multiple related genomes. These might be clinical isolates of the same species exhibiting different pathogenetic properties, environmental isolates from different sites, or a study over time of the changes…

  • Automatically displaying open reading frames with MacVector’s Scan For Open Reading Frames tool

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    Chris
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    As well as Scan for.. Missing Features that shows annotation on your sequences, you may have noticed extra CDS features annotated to your sequences. These are from the Scan for.. Open Reading Frames tool that automatically scans every DNA sequence window for open reading frames and displays the results in the Map tab. It’s very useful,…

  • 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 (for example InterProScan). Very useful for when you want to view more detailed or updated information. Within the Genbank specification, which MacVector extensively uses,…

  • Use the Replica Button For Synchronized Views

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    Chris
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    Most primary MacVector windows (Nucleic Acid Sequence, Protein Sequence, Multiple Sequence Alignment, Align To Reference, Contig Assembly etc.) have a Replica toolbar button. If you click that button, a second window will open, potentially set to a different tab. The key to this functionality is that the two windows are linked – any selections you…