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!

Tag Archives: pcr

What can MacVector do for me?

Here’s what MacVector can do for your lab. Comparing sequences Whatever type of alignment your sequence needs, there’s a tool in MacVector. CRISPR Indel Analysis: Identify insertions and deletions following CRISPR editing of a target. Sequence assembly of NGS data against a reference genome or compare your sequencing against your new construct. Translated Multiple Sequence […]

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Adding a primer to MacVector’s Primer Database.

  MacVector’s Primer Database tool makes it easy to store your lab’s regular primers. It allows you to save and retrieve primers from the Primer Database from the Primer3 and Quicktest Primer tools. You can also scan sequences for potential primer binding sites. The Primer Database will also store tails and allow you to specify […]

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Annotating primers to your sequence with MacVector

Designing a pair of primers to amplify a single feature is pretty quick with MacVector. Once you have designed a pair of primers with MacVector, you can quickly annotate both the primers and product to your sequence template. The annotation contains a timestamp and the primer’s characteristics. It also contains the full sequence of the primer, […]

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Testing pairs of primers with MacVector

MacVector’s Primer Design tools makes it easy to test your primers. You can insert them directly from MacVector’s Primer Database or copy and paste them. Tweet

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A whole new way to design primers with MacVector’s Quicktest Primer

QuickTest Primer completely changes the way primers can be designed on a computer. It simplifies primer design by showing your primer and its statistics in realtime. Does your primer have a hairpin? Nudge it along your template until the hairpin goes? Want to add a restriction site? Then add one and again nudge your primer […]

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What can MacVector do for your lab?

Here’s an overview of what MacVector can do for you! Comparing sequences Whatever alignment your sequence needs, MacVector has the right tool. CRISPR Indel Analysis: Identify insertions and deletions following CRISPR editing of a target. Multiple sequence alignment of protein or DNA sequences using CLustalW/Muscle or T-Coffee and produce publication quality alignments. Sequence assembly of […]

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Generating a primer report to send to your Oligo Synthesis service

QuickTest Primer is a great tool for primer design. Paired with Primer Design/Test (Pairs) it gives you great control and flexibility for designing primers with tails, mismatches, silent mutations, one out sites and more. Once you’ve designed your primer the next step is to get it synthesized. QuickTest Primer will produce a PDF report of […]

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Using QuickTest Primer to check for hairpins in sequences, and not just primers.

Although QuickTest Primer is intended for designing primers, the interface is very flexible. If your sequence is not too long, you can use the Quickest Primer interface to scroll through a sequence and visually look for hairpins appearing in the hairpin pane. The easiest way to do this is to select the first ~100 nt […]

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Create your own Primer Database.nsub from an Excel spreadsheet

Wouldn’t it be great if there was an easy way of converting that huge primer collection you have into a format that MacVector can use? Well, luckily there is! There is a utility called “Primer Converter” that you can download from our website. To use the utility you first need to get your primers into […]

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Use Analyze->Primer Database Search to scan sequences for primer binding sites

It’s easy to keep track of all your primers using a MacVector subsequence (.nsub) file. We even ship MacVector with a starter file called “Primer Database.nsub” that you can find in the /Applications/MacVector/Subsequences/ folder. If you choose Analyze | Primer Database Search… and use this default file to search pUC19, you’ll find many of the […]

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