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Restriction enzyme analysis in MacVector and REBASE
Read more: Restriction enzyme analysis in MacVector and REBASEAlthough there are two different ways to perform restriction enzyme analysis with MacVector, there are also additional places where restriction enzyme sites are shown. All these tools use the same set of restriction enzyme files to recognise enzymes. These files are updated regularly from the REBASE database. The restriction enzymes are divided into multiple files.…
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Drag and drop to quickly annotate ORFs
Read more: Drag and drop to quickly annotate ORFsYou 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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101 things you (maybe) didn’t know about MacVector: #50 – Using Align To Folder to “clone” genes from NGS data
Read more: 101 things you (maybe) didn’t know about MacVector: #50 – Using Align To Folder to “clone” genes from NGS dataThe Database | Align To Folder… function in MacVector is remarkably powerful. Its like having your own personal BLAST search except that it can also scan through millions of Reads in fasta or fastq formatted files to identify those matching an input sequence, which can be DNA OR protein. In addition, it understands about paired-end…
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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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How to change the default appearance of RE sites
Read more: How to change the default appearance of RE sitesMacVector 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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NIH Research Festival September 14-16, 2016
Read more: NIH Research Festival September 14-16, 2016We’re at the NIH Research Festival this week. Please drop by our booth on Thursday or Friday, when the big, white exhibitors tent is open. We’re on booth #562. We’ll be able to show you our latest release, MacVector 15 and we’ll have some goodies too!
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Working with digested fragments in the Cloning Clipboard
Read more: Working with digested fragments in the Cloning ClipboardThe 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
Read more: 101 things you (maybe) didn’t know about MacVector: #49 – Identifying CRISPR IndelsIf 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
Read more: How to use Codon Preference plotsWhen 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.
Read more: 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…
