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How to find and open all the sequences on your computer containing a specific gene.
Read more: How to find and open all the sequences on your computer containing a specific gene.How often have you had a vector or sequence open and thought “I’m sure I have other vectors with that gene, but I can’t remember where they are”? If you are using MacVector 13.5, its very easy to quickly search folders on your hard drive to find all the sequences that contain that gene, then…
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How to identify methylation blocked Restriction Sites
Read more: How to identify methylation blocked Restriction SitesMacVector currently does not have a built-in function for recognizing restriction sites that are blocked by the DAM or DCM methylases. However, there is a simple workaround that lets you visually identify those sites in the restriction enzyme analysis result windows. The basic idea is that you create additional restriction enzyme sites for each enzyme…
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Downloading BLAST Hits from the NCBI
Read more: Downloading BLAST Hits from the NCBIWhen you use MacVector to run a BLAST search, did you know that you can download any matching sequences directly from the BLAST Description List window? Simply select text on any part of the line(s) representing the sequence you want to download and choose Database | Retrieve To Desktop or Database | Retrieve To Disk…
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Creating cloning construction flowcharts in third party applications
Read more: Creating cloning construction flowcharts in third party applicationsWe’ve previously discussed how every ligation is documented. You get a “Frag” annotation that contains the date, source sequence, enzymes used and any end modification that was done to that fragment during the ligation. However, we had regular requests to make it easier for user to document their constructs in other ways. For example being…
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Clearing the “find” history in the Primer and Find dialogs.
Read more: Clearing the “find” history in the Primer and Find dialogs.Many tools in MacVector store a history of sequences, or search terms, that you have previously used. For example the Find dialog and Primer Design tools. This is accessed using a drop down menu to the right of the box where you would normally type, or paste, your sequence. This is to allow easy access…
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Simulated Agarose Gels
Read more: Simulated Agarose GelsMacVector 14.5 has a Agarose Gel interface which allows you to view photo-realistic recreations of restriction digests of linear and circular DNA molecules. The gels look so realistic that users have had a hard time telling photos of their own digests from the simulation in MacVector. When you first use the new tool and compare…
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Cloning Clipboard: A few tips on working with digested fragments
Read more: Cloning Clipboard: A few tips on working with digested fragmentsThe Cloning Clipboard is an easy, and flexible, way to design and document your cloning strategies. Recently we discussed how every ligation in a cloning procedure is documented and stored in a sequence, so you always know how a construct was made. If you need to manipulate a fragment as a sequence, before ligating it,…
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How Assembler uses quality scores to create assemblies
Read more: How Assembler uses quality scores to create assembliesA common problem with all types of sequence assembly is distinguishing between sequencing errors and true genomic variations. Quality scores are one way to help the algorithm identify if a variation is of high quality and therefore likely to be a SNP or a sequencing error. For Assembler trace files can be basecalled with Phred,…
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Visualising ORF analysis results in the MAP tab.
Read more: Visualising ORF analysis results in the MAP tab.The Map tab of MacVector is a powerful way to visualise and interact with your sequences. All analysis tools will work directly in the Map tab. You can design primers, ligate and digest fragments from the Cloning Clipboard, visualise translated CDS regions and much more. In fact one of the only tasks, you will need…
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Cloning Clipboard: Documenting the history of a construct
Read more: Cloning Clipboard: Documenting the history of a constructDesigning and documenting cloning strategies is easy with the Cloning Clipboard. You can perform quite complex ligations by simply dragging compatible ends together. Not only that but every step is documented and recorded in the resulting sequence, so you always know where each fragment came from. Ligating a single fragment into a vector is as…
