Team:UTP-Software/Tutorial

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S2MT_championship Tutorial

S2MT Tutorial - Primer Creation

    Img1.png


    (S2MT) GUI parts:

  • 1. URL/DNA Sequence textbox: This is the main input.
  • 2. Standard selection: We can select the desired standard and the program will check the compatibility with it.
  • 3. Process button: After giving the inputs, analyze the sequence.
  • 4. Primer textbox: Here we get the output.
  • 5. Notification area: The script's feedback.

    Some points to take in consideration:

  • The primer's starting positions will appear in the MATLAB's console.
  • The sequence box can either get an URL from the Parts Registry pointing to a specific Part or a DNA sequence (the textbox is case insensitive).
  • Some PartsRegistry Devices does not have it corresponding DNA Sequence on it.
  • Be sure that the DNA Sequence you put in the box does not contain any other letter than 'a', 't', 'g' and 'c'.
  • Some sequence's incompatibility can't be fixed.
    Fix.png

    (S2MT) succesfully fixing the incompatibility of the given DNA sequence with the standard 21.


    To download the script go to: https://github.com/igemsoftware/UTP_Software_2012 and get all three files.

    Files descriptions:

  • S2MT.m: Does all the sequence analysis process.
  • S2MT_G.m: Code for the grafical interface. (Run this)
  • S2MT_G.fig: Binary file for the grafical interface.

    • Note that (S2MT) relies on the Bioinformatics Toolbox of MATLAB (both supplied by iGEM) to make its computations, so you need the toolbox to be able to run the script.

You can download this tutorial here: https://static.igem.org/mediawiki/2012/2/29/S2MT_Tutorial.pdf

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