diff --git a/wiki/pages/software.html b/wiki/pages/software.html index 684a0a2203314eb0483c3604744c54790864cec6..e4003757af842736a99faf970d7c535405a35c21 100644 --- a/wiki/pages/software.html +++ b/wiki/pages/software.html @@ -125,6 +125,7 @@ </p> <div class="image-container"> <img src="https://static.igem.wiki/teams/4864/wiki/software/4.png" alt="P4" style="width: 50%; height: auto;"> + </div> </section> <section class="desc-section"> @@ -138,6 +139,83 @@ <div class="image-container"> <img src="https://static.igem.wiki/teams/4864/wiki/software/5.png" alt="P5" style="width: 50%; height: auto;"> </div> + <p>If no RBS is found in the reverse direction, it will display a message indicating that “NO RBS SEQUENCE FOUND IN REVERSE DIRECTION†+ <br> + 7. Clear Entry: + You can click the "CLEAR ENTRY" button to clear the input field and start a new analysis. + <br> + 8. Repeat Analysis: + You can repeat the analysis by entering a new DNA sequence and clicking the "FIND" button again. + <br> + 9. Close the GUI: + You can close the GUI window when you are done with the analysis. + </p> + </div> + </section> + <section class="desc-section"> + <h2>PromoterStrengthPredict 2.0</h2> + <p>“PromoterStrengthPredictâ€, a tool developed by our alumni of the SVCE-CHENNAI 2017 team, adapts a machine learning approach to predict the strength of Sigma 70 promoters in E. coli, thus streamlining and enhancing promoter selection for the iGEM projects. We developed an upgraded version of this software, “PromoterStrengthPredict 2.0â€, which involves finding the RBS strength when the sequence is given as the input. The output will be a 2-D plot between the RBS sequence score (X-axis) and the RBS strength value (Y-axis). + <br> + Here's a step-by-step protocol to use and get the output from this code: + <br> + 1. Install Required Libraries:<br> + Ensure that you have the necessary Python libraries installed. You need to have matplotlib.pyplot, Pylab, Numpy, Biopython, and Bio installed. You can install them using pip if they are not already installed. + <br> + 2. Enter Promoter Sequence: + <br> + <ul> + <li>Enter the newly characterized data to be added to the dataset. </li><br> + <li> Enter the promoter sequence you want to analyze into the input field. (The sequence can only contain the characters 'A,' 'C,' 'G,' and 'T.' Other characters are not allowed.) </li><br> + <li>The executed code will give you the following results:<br> + -Theta value<br> + -Predicted promoter strength<br> + -predicted ln strength<br> + -R<sup>2</sup> value<br> + -Adjusted R<sup>2</sup> value<br> + </li><br> + </ul> + </p> + <div class="image-container"> + <img src="https://static.igem.wiki/teams/4864/wiki/software/p2-1.png" alt="p2-1" style="width: 50%; height: auto;"></div> + </section> + <section class="desc-section"> + <p> + 3. Enter RBS Sequence:<br> + <ul> + <li>Enter the newly characterized data to be added to the dataset. </li><br> + <li> Enter the RBS sequence you want to analyze into the input field. (The sequence can only contain the characters 'A,' 'C,' 'G,' and 'T.' Other characters are not allowed.) </li><br> + <li>The executed code will give you the following results:<br> + -Theta value<br> + -Predicted RBS strength<br> + -predicted ln strength<br> + -R<sup>2</sup> value<br> + -Adjusted R<sup>2</sup> value<br> + </li><br> + </ul> + <div class="image-container"> + <img src="https://static.igem.wiki/teams/4864/wiki/software/p2-2.png" alt="p2-2" style="width: 50%; height: auto;"></div> + </p> + </section> + <section class="desc-section"> + <p> + 4. Plot Analysis:<br> + The program will analyze the sequences of the RBS (ribosome binding site) and the promoter region and generate a 3-D scatter plot for promoter strength and a 2-D plot for RBS strength prediction.<br> + The 3-D scatter plot for the promoter strength prediction includes the following information:<br> + <ul> + <li>-35 Hexamer score (X-axis)</li> + <li>-10 Hexamer score (Y-axis)</li> + <li>Promoter strength (Z-axis)</li> + </ul> + <div class="image-container"> + <img src="https://static.igem.wiki/teams/4864/wiki/software/p2-3.png" alt="p2-3" style="width: 50%; height: auto;"></div> + The 2-D plot for the RBS strength prediction includes the following information:<br> + <ul> + <li>RBS sequence score (X-axis)</li> + <li>RBS strength (Y-axis)</li> + </ul> + </p> + <div class="image-container"> + <img src="https://static.igem.wiki/teams/4864/wiki/software/p2-4.png" alt="p2-4" style="width: 50%; height: auto;"></div> </section> </section>