General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Monthly Archives: August 2016

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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101 things you (maybe) didn’t know about MacVector: #49 – Identifying CRISPR Indels

If you are screening a set of clones for the presence of changes after a CRISPR experiment, then the MacVector Analyze | Align To Reference functionality is the approach to use. However, you may find that the default parameters are not ideal for this type of analysis – they are tuned for simple sequence confirmation […]

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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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MacVector 15 is out, with a focus on protein analysis and alignment tools.

MacVector 15 has many new features including new protein analysis tools for reference alignment of proteins, translated DNA alignments and for functional analysis of protein sequences. InterProScan: Scan proteins for functional domains against a variety of sequence, protein family, domain and motifs databases using the InterProScan service. This performs a search against many different databases […]

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