Team:UTP-Software/SoftwareTool
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In some cases, it’s impossible to fix some sequences, because based on the protocol, the output primer may not comply with the steps that are listed in the “Protocol Followed to design the primers” section. Meaning that another standard should be selected. </ul></div> | In some cases, it’s impossible to fix some sequences, because based on the protocol, the output primer may not comply with the steps that are listed in the “Protocol Followed to design the primers” section. Meaning that another standard should be selected. </ul></div> | ||
- | ==== Flow diagram for the S<sup>2</sup>MT ==== | + | ==== Flow diagram for the S<sup>2</sup>MT - Primer Design Section ==== |
[[File:Flow diagram.png|center]] | [[File:Flow diagram.png|center]] | ||
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==== Protocol Followed to design the primers:<sup>[http://web.physics.ucsb.edu/~deborah/pro/pro_pdf/Stratagene%20QuikChange.pdf]</sup> ==== | ==== Protocol Followed to design the primers:<sup>[http://web.physics.ucsb.edu/~deborah/pro/pro_pdf/Stratagene%20QuikChange.pdf]</sup> ==== | ||
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<li> Primers need not be 5´ phosphorylated but must be purified either by fast polynucleotide liquid chromatography (FPLC) or by polyacrylamide gel electrophoresis (PAGE). Failure to purify the primers results in a significant decrease in mutation efficiency.</li> | <li> Primers need not be 5´ phosphorylated but must be purified either by fast polynucleotide liquid chromatography (FPLC) or by polyacrylamide gel electrophoresis (PAGE). Failure to purify the primers results in a significant decrease in mutation efficiency.</li> | ||
<li> It is important to keep primer concentration in excess. Stratagene suggests varying the amount of template while keeping the concentration of the primer constantly in excess.</li></ul></div> | <li> It is important to keep primer concentration in excess. Stratagene suggests varying the amount of template while keeping the concentration of the primer constantly in excess.</li></ul></div> | ||
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== Next S<sup>2</sup>MT Version == | == Next S<sup>2</sup>MT Version == | ||
<div align="justify">After finishing the first version, we had in mind several things to implement to the next: | <div align="justify">After finishing the first version, we had in mind several things to implement to the next: | ||
- | <ul><li> | + | <ul><li> Our next version will for sure incorporate a "ab1" chromatogram file reader, because right now we are relying on phred files, which eventhoug phred scores are pretty accurate, not every sequencing company provide those. |
- | + | Some bugs are still to be fixed, and some performance improvement can also be a part of the next version. | |
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- | <li>Our Second idea is | + | <li>Our Second idea (still under development) is about adding a whole new tool to our software, and thats what we call BioSinergia (spanish for "BioSinergy"), which will be like a smart database of metabolic rutes that is going to help teams and researchers to work and study the production of bioenergy through synthetic biology. This project will make use of our S<sup>2</sup>MT tool to make it easy for new iGEM teams to work with biofuels in their projects. |
</ul></div> | </ul></div> | ||
Latest revision as of 03:47, 27 October 2012
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