Category: Tips
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Estimating insert length quickly for a read pair
[Edit December 20, 2017 – As of MacVector 15.5 you can simply right click a READ and select “SEE MATCHING READS” to view the pair of reads. The total sequence length is selected. ] Insert length is the length of the sequence in between a pair of reads. Sequencers are supplied DNA samples in fragments of…
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Drag and drop to quickly annotate ORFs
You can use the Analyze | Open Reading Frames function to very quickly find ORFs on a sequence. Did you know that you can very quickly turn those results into permanent CDS features on your sequence? After running the Open Reading Frames analysis, simply drag and drop the ORF objects you are interested in from…
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Download the latest published version of your favorite sequence with its accession number
It’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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How to change the default appearance of RE sites
MacVector is extremely customizable. If you don’t like the defaults we supply, its very easy to change them. Lets look at restriction enzyme sites. By default we show unique sites in small red letters and sites that cut more than once in small blue letters. But suppose you want something bigger, bolder and, well, more…
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Working with digested fragments in the Cloning Clipboard
The Cloning Clipboard is an easy, and flexible, way to design and document your cloning strategies. Here’s two tips on manipulating a single fragment. – If you drag a fragment from the Cloning Clipboard to a vector, then you’ll get the ligation dialog. However, if you have already selected a pair of enzyme sites, then…
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How to use Codon Preference plots
When you are looking for open reading frames in newly sequenced regions, it’s not always the longest ORFs that are protein-encoding. Lets look at an example from one of the sequences included with MacVector: /Applications/MacVector/Sample Files/Gal Cosmid.nucl. This is from Streptomyces coelicolor, a filamentous bacteria with a 73% G+C content. The high G+C% means that…
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Tweak your DNA Matrix for better Align To Folder searches with primers
You can use the Database | Align To Folder function as your own “personal BLAST search”, comparing a sequence to all of the sequences in a target folder hierarchy. The files in the folder can be in any format MacVector recognizes, including fasta and fastq formatted multiple sequence files. Many users take this approach to…
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How to reset the sequence numbering when working with a subsection from a larger sequence
When you copy a section from a long sequence and paste it into a new MacVector window, the original numbering from the original sequence is retained. This is very useful if you want to work on a shorter segment of a genome without losing the original numbering. However, sometimes it is preferable to have the…
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Organising your sequences using Smart Folders
OS X’s Finder has many features for quickly finding and working with your files. Spotlight Search is one such tool that most Mac users are familiar with. However, Smart Folders is a tool that is very useful but often overlooked. Smart Folders allow you to create a dynamic folder whose contents are derived from a…
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How to increase the number of graphics levels to stop features overlapping.
MacVector tries to optimize the Map graphics layout using a trade-off between performance and minimizing unnecessary white space. Sometimes the default settings we have chosen are not ideal, particularly if you are looking at the Map tab of an Align To Reference window where you have a large number of reads overlapping the same region.…