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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…
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Tweak your DNA Matrix for better Align To Folder searches with primers
Read more: Tweak your DNA Matrix for better Align To Folder searches with primersYou 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
Read more: How to reset the sequence numbering when working with a subsection from a larger sequenceWhen 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…
