Team:UTP-Software/SoftwareTool
From 2012.igem.org
Line 27: | Line 27: | ||
== '''S<sup>2</sup>MT Tutorial''' == | == '''S<sup>2</sup>MT Tutorial''' == | ||
+ | <div align="justify"><ul> | ||
+ | [[File:Img1.png]] | ||
- | '' | + | |
+ | (S<sup>2</sup>MT) GUI parts: | ||
+ | <li>1. URL/DNA Sequence textbox: This is the main input.</li> | ||
+ | <li>2. Standard textbox: The assembly reference we are working on.</li> | ||
+ | <li>3. Process button: After giving the inputs, analyze the sequence.</li> | ||
+ | <li>4. Primer textbox: Here we get the output.</li> | ||
+ | <li>5. Notification area: The script's feedback. | ||
+ | </li></ul></div> | ||
+ | |||
+ | <div align="justify"><ul> | ||
+ | (S<sup>2</sup>MT) 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. | ||
+ | |||
+ | Some points to take in consideration: | ||
+ | |||
+ | <li>The primer's starting positions will appear in the MATLAB's console. | ||
+ | <li>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).</li> | ||
+ | <li>Some PartsRegistry Devices does not have it corresponding DNA Sequence on it.</li> | ||
+ | <li>Be sure that the DNA Sequence you put in the box does not contain any other letter than 'a', 't', 'g' and 'c'.</li> | ||
+ | <li>Some sequence's incompatibility can't be fixed. | ||
+ | </li></ul></div> | ||
+ | |||
+ | |||
+ | [[File:Fix.png]] | ||
+ | |||
+ | (S<sup>2</sup>MT) succesfully fixing the incompatibility of the given DNA sequence with the standard 21. | ||
== Next S<sup>2</sup>MT Version == | == Next S<sup>2</sup>MT Version == |
Revision as of 13:30, 26 September 2012
Home | Team & Attributions | Project | S2MT | Tutorial | Biosinergia | Notebook | Human Practices | Safety | Sponsors |
---|
|
Project DetailsWhat is the S2MT tool?
The SynBio Sequence Mutation Tool (S2MT) it's a MATLAB implementation software that helps teams to start their projects once they have selected some possible BioBricks or DNA sequences to work with. This tool was developed in MATLAB basically for the reason that, what new iGEM teams require is a flexible environment capable of not only running the algorithm that we develop, but also a place where they can continue working their ideas, examine more in detail their sequences and even continue the development of our tool. So we thing that our system will also knock down the barriers that exist between computation and biology and give students the tools required to do better simulations, and save a lot of valuable time! Behind the code there are three simple steps in which the program consists: Protocol Followed to design the primers:[1]
Tm = 81.5 + 0.41(%GC) − 675 / N - where N is the primer length in base pairs. S2MT Tutorial
(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. Some points to take in consideration: (S2MT) succesfully fixing the incompatibility of the given DNA sequence with the standard 21. Next S2MT VersionReferences[1]. Stratagene. QuikChange™ Site-Directed Mutagenesis Kit. Catalog #200518. Revision #108005h. Available in: [1]. |