Tag: primer3

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

    —

    by

    admin
    in

    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…

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

    —

    by

    Chris
    in

    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…

  • Create your own Primer Database.nsub from an Excel spreadsheet

    —

    by

    Chris
    in ,

    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…

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

    —

    by

    Chris
    in

    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…

  • Using the Primer Database to store your lab’s collection of primers

    —

    by

    Chris
    in

    MacVector’s Primer Database allows you to save and retrieve primers from a Primer Database with the Primer3 and Quicktest Primer tools. You can also scan sequences for potential primer binding sites using Primer Database Search. The tool comes with a starter database of primers, but you can use existing subsequence files or import primers from…

  • Generating a primer report to send to your Oligo Synthesis service

    —

    by

    Chris
    in

    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…

  • Testing pairs of primers

    —

    by

    Chris
    in

    Quite a few versions back MacVector used to have an old, but well loved, Test PCR Primer Pairs algorithm. Its interface was clunky and it did not take into account modern algorithms for calculating Tm. However, the results were useful. If you liked this tool then you will be pleased to know that the functionality…

  • Clearing the history in the Primer and Find dialogs

    —

    by

    Chris
    in

    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…

  • Calculating the PCR annealing temperature for a pair of primers

    —

    by

    Chris
    in

    MacVector not only calculates the melting temperature (Tm) for any primers you design, but also displays the recommended annealing temperature (Ta) that you should use in PCR experiments using those primers. You can access the main MacVector interface for designing pairs of primers using Analyze | Primer Design (Primer3). From here you can ask MacVector…

  • Using the Primer Database to store your lab’s collection of primers

    —

    by

    Chris
    in ,

    MacVector 14 saw the introduction of the new Primer Database tool. This 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 tool comes with a starter database of primers, but you can use existing subsequence…