Author: Chris
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Use Analyze->Primer Database Search to scan sequences for primer binding sites
It’s easy to keep track of all your primers using a MacVector subsequence (.nsub) file. We even ship MacVector with a starter file called “Primer Database.nsub” that you can find in the /Applications/MacVector/Subsequences/ folder. If you choose Analyze | Primer Database Search… and use this default file to search pUC19, you’ll find many of the…
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Batch auto annotation of blank sequences with MacVector and AppleScript
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…
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MacVector For Windows update
It’s been some time since since the last update about MacVector for Windows, although development has certainly not been quiet. Here’s some screenshots. Graphical Map Sequence Editor Automatic Restriction Enzyme and ORF Analysis Primer Design Cloning Clipboard
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Using the Primer Database to store your lab’s collection of primers
MacVector’s Primer Database allows you to save and retrieve primers from a Primer Database with the Primer3 and Quicktest Primer tools. You can also scan sequences for potential primer binding sites using Primer Database Search. The tool comes with a starter database of primers, but you can use existing subsequence files or import primers from…
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Viewing external database entries for features in a sequence.
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,…
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Optimizing the Reverse Translation function
The Analyze | Reverse Translation menu option lets you create a DNA sequence from a Protein sequence, reverse translated using a specific Genetic Code (by default, the Universal Genetic Code). The default option creates a DNA sequence with N’s and other ambiguities reflecting the degeneracy of the genetic code. This is great if you want…
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Tear-off Result Window Tabs: make viewing results easier.
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…
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IMPORTANT SERVICE ANNOUNCEMENT Entrez and BLAST services will stop working in November for MacVector 15.0.3 and earlier.
UPDATE – November 8, 2016 – Although the official switch off date is not until Wednesday the 9th, Entrez and BLAST are NOT currently working from MacVector 15.0.3 and earlier. We suspect this change is now permanent. UPDATE – November 7, 2016 – We have just been notified by the NCBI that they will be…
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Highlighting sequence using color and lower case in the Editor tab
You can very quickly annotate a region of interest in your sequence in the Editor tab. For example, showing introns in lower case or highlighting CDS features with a colored background. Using the TRANSFORMATIONS menu To enter sequences as mixed case. Enable Edit | Transformations | Enable Mixed Case Entry Type your sequence using SHIFT…