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Simple but accurate restriction enzyme based clone construction using Copy and Paste
Read more: Simple but accurate restriction enzyme based clone construction using Copy and PasteThe quickest and simplest way to create restriction enzyme generated constructs in MacVector is to use Edit | Copy and Edit | Paste. The strategy to use is identical to copying a paragraph from one Microsoft Word document to insert into a second document. i.e. Select the restriction enzymes flanking the source fragment in either…
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How to change the default appearance of features
Read more: How to change the default appearance of featuresIf you download a sequence from Entrez, or open a sequence that is not in MacVector format, MacVector assigns a default appearance to any features on the sequence. For example, CDS features are shown as a blue arrow with a Helvetica 9 point font label. With the advent of ultra high resolution displays, you may…
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Use File->Export in the Contig Editor to save selected reads
Read more: Use File->Export in the Contig Editor to save selected readsLast week we covered the fact that you can use File->Export to save sequences or alignments in different formats. Delving down deeper into this, some of the views will save different types of data based on what you select in the format menu. The best example of this is the Contig Editor. If you choose…
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Use File->Export to save sequences in a different file format
Read more: Use File->Export to save sequences in a different file formatOver the years, Apple have changed the recommended layout and functionality of the File menu. At MacVector, we always try to follow Apple’s guidelines wherever possible so that new users will feel comfortable with familiar menus. However, long-term users may experience some confusion, particularly if you want to save sequences in a different format. Here…
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How to reset the graphics palette if it disappears
Read more: How to reset the graphics palette if it disappearsThe floating graphics palette is extremely useful for helping to configure the display of the Map tab. You can easily toggle the visibility of any individual or group of features and adjust many aspects of the display. MacVector does try to remember the last position you moved this to so its there ready for you…
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Tips for finding ORFs in your sequence
Read more: Tips for finding ORFs in your sequenceWe’ve talked in previous tips about annotating open reading frames as CDS features. However, what if your sequence has no annotated ORF? MacVector’s ANALYZE | OPEN READING FRAMES… tool will help you find any quickly. However, if you are new to this tool there are a few options that may prove initially confusing. These options…
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Using QuickTest Primer to check for hairpins in sequences, and not just primers.
Read more: Using QuickTest Primer to check for hairpins in sequences, and not just primers.Although QuickTest Primer is intended for designing primers, the interface is very flexible. If your sequence is not too long, you can use the Quickest Primer interface to scroll through a sequence and visually look for hairpins appearing in the hairpin pane. The easiest way to do this is to select the first ~100 nt…
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Download the latest published version of your favorite sequence with its accession number
Read more: Download the latest published version of your favorite sequence with its accession numberIt’s very quick to download the latest version of a sequence if you know its accession number. When you start working with a new sequence, it’s the best place to start. Go to DATABASE > ENTREZ Enter the accession number of your favorite sequence Click SEARCH Double click on the result to open up your…
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Customizing BLAST alignment results to make mismatches more noticeable
Read more: Customizing BLAST alignment results to make mismatches more noticeableWhen you run a Blast search, as well as a list of hits, you will get a list of alignments between your query sequence and each hit. As with most other text alignments in MacVector, identical matches are by default represented by a vertical line (a score greater than 1) and mismatches (whether similar or…
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How to save contig consensus sequences from assembly projects
Read more: How to save contig consensus sequences from assembly projectsThe MacVector Assembler module lets you create projects, populate them with Sanger Sequencing or NGS data files (or any sequences in a format that MacVector can read) and then assemble them using the popular phrap and/or Velvet assemblers. Typically, the result will be a collection of contigs that you might want to use in additional…
