Working From Home – common workflows

During the Covid-19 pandemic we want to ensure that you have access to the MacVector license that you would use in the lab, especially if you are working from home. If you use MacVector, even an older version, and are having trouble activating it (or installing it) at home email MacVector Support and we will help. If you are in anyway connected with COVID19 research, then please have our thanks, and have an annual license free of charge.

If you are working from home then here’s a series of blog posts to familiarize you with tools that you may never have used before. You may have just been using MacVector to design PCR primers, but since you do not have a PCR machine on the kitchen table, then here’s what else MacVector can do for you. This week we’ll cover the many common workflows that the molecular biologist may need.

Cloning constructs

Select two restriction sites and click DIGEST. Drag the digested fragment from the Cloning Clipboard to your vector and click LIGATE.

Gibson Assembly/Ligase Independent Cloning

FILE | NEW | GIBSON/LIGASE INDEPENDENT ASSEMBLY. Choose the type of project, add a cloning vector, then drag a gene from a sequence to clone.

Designing primers

Select a short region of sequence. Click ANALYZE | QUICKTEST PRIMER. Add a restriction site or mutation, slide the primer until the oligo is optimal.

Testing primers

Open your template sequence, Go to ANALYZE | PRIMER DESIGN/TEST(PAIRS). For the left primer click USE THIS Primer. Type or paste in your forward primer, Repeat for the reverse primer. Click TEST

Agarose Gel Simulation

Select FILE | NEW | AGAROSE GEL, Drag a restriction site from the Map tab of a sequence and drop on the Agarose Gel window

Comparing sequences

Select FILE | NEW | ALIGNMENT, Click ADD SEQS and then ALIGN.

List genetic differences between one organism and another related strain

Open two genomes and run ANALYZE | COMPARE GENOMES BY FEATURE..

Searching for your sequence.

Select DATABASE | ONLINE KEYWORD SEARCH (ENTREZ) , enter the accession number of your favorite gene and hit search. Double click the hit to open it directly in MacVector.

Annotating sequences

Right click (or CTRL+left Click) on any faded ORF or Feature on your sequence. Select CREATE FEATURE.

To align a small sequencing project against a reference.

Run FILE | NEW | ALIGN SEQUENCES TO A REFERENCE... Choose a reference sequence, then add your trace files from the sequencing facility and click ALIGN.

De novo assembly of sequencing reads

Run FILE | NEW | ASSEMBLY PROJECT, Choose a reference sequence, add your sequencing reads and also any reference sequences.

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