Team:AMU-Poznan/Modeling

From 2014.igem.org

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</br> Here we present Survey results and Modeling results (for Modeling results please scroll down the page)</br>
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<p>We decided to pay more attention to model sh-miR molecules with different RNA 2D structure prediction software (we use RNAfold in our software). Soon we will publish our results!</p>
 
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<br /><h1>Survey</h1><br /><br />
14.10.2014<br />
14.10.2014<br />
31 survey responses:<br />
31 survey responses:<br />
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</br></br>and age</br></br>
</br></br>and age</br></br>
<img src="https://static.igem.org/mediawiki/2014/8/89/Chart3.png" width="60%"></br>
<img src="https://static.igem.org/mediawiki/2014/8/89/Chart3.png" width="60%"></br>
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<h3>Conclusions</h3>
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Knowledge of RNAi is good. however people do not know what exactly sh-miR is.</br>
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Users are eager to wait up to 8h, 24h only 50% and 2 days only 20% (work without software will take 2 days).</br>
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What are the most important features of bioinformatic software:</br>
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user-friendly interface</br>
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documentation</br>
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easy user-guide</br>
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fast response from software</br></br>
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what is important in shmiR designer:</br>
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speed of software</br>
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possibilty to choose miRNA scaffold</br>
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experimental evaluation</br>
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</br></br></br>
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<h1>Modeling</h1>
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</br>
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<p>We decided to pay more attention to model sh-miR molecules with different RNA 2D structure prediction software (we use RNAfold in our software). Here are our results (however we only show modeling of one molecule the conclusions are obvious - we performed folding for over 10 molecules):</p>
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</br></br>
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example analyzed sequence:
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</br>CTAAAGAAGGTATATTGCTGTTGACAGTGAGCGACTGUUUGUAUUCGCCCUAGCGCCTGTGAAGCCACAGATGGGGCGCUAUGGCGAAUACAAACATGCC</br>TACTGCCTCGGACTTCAAGGGGCTACTTTAGGAGCA</br>
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We always take first generated structure made with default options</br>
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If there is difference in algorithm we always take RNA folding over DNA folding</br>
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mfold</br>
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<img src="https://static.igem.org/mediawiki/2014/2/20/Mfold.png" width="60%">
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</br>
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RNAstructure</br>
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<img src="https://static.igem.org/mediawiki/2014/2/22/RNAstructure.jpeg" width="60%">
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</br>
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RNAfold</br>
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<img src="https://static.igem.org/mediawiki/2014/6/61/Rnafold.png" width="60%">
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<img src="" width="60%">
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<img src="" width="60%">
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<img src="" width="60%">
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<h3>Conclusions</h3>
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Different algorithms gives very different results. To have the most reliable structure it recommended to check the structure</br>
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with different software.</br>
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</br>
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Latest revision as of 21:02, 16 October 2014

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