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<h3>SOFTWARE</h3>
<h2>SeqPredict</h2>
<p>
- “SeqPredict†is a machine learning-based tool developed by the iGEM team, SVCE-CHENNAI 2023. We aim to streamline the process of gene circuit design and assembly, saving teams valuable time and effort by developing software that can locate RBS, Anderson Promoter Regions, and Flanking Regions within a given DNA sequence. These biobricks play an important role in the design and development of successful synthetic biology projects.
+ “SeqPredict†is a machine learning-based tool developed by the iGEM team, SVCE-CHENNAI 2023. We aim to streamline the process of gene circuit design and assembly, saving teams valuable time and effort by developing software that can locate RBS, Anderson Promoter Regions, and Flanking Regions within a given DNA sequence. These biobricks play an important role in the design and development of successful synthetic biology projects. </p>
- The developed code provided below is a Python program that uses biopython and the Tkinter library to create a graphical user interface (GUI) for analyzing the location of DNA features such as RBS, Start Codon, and Flanking DNA sequences.
+ <p>The developed code provided below is a Python program that uses biopython and the Tkinter library to create a graphical user interface (GUI) for analyzing the location of DNA features such as RBS, Start Codon, and Flanking DNA sequences. </p>
- It searches for a specific DNA motif (RBS - Ribosome Binding Site) and identifies its position in both the forward and reverse directions. Additionally, it calculates the length of the flanking region and checks whether it falls within an ideal range.
+ <p>It searches for a specific DNA motif (RBS - Ribosome Binding Site) and identifies its position in both the forward and reverse directions. Additionally, it calculates the length of the flanking region and checks whether it falls within an ideal range.</p>
- Here's a step-by-step protocol to use and get the output from this code:
+ <p>Here's a step-by-step protocol to use and get the output from this code:</p>
+ <p>1. Install Required Libraries:</p>
+ <p>Ensure that you have the necessary libraries installed. You need to have Tkinter, Biopython, and Bio installed. You can install them using pip if they are not already installed.</p>
- 1. Install Required Libraries:
- Ensure that you have the necessary libraries installed. You need to have Tkinter, Biopython, and Bio installed. You can install them using pip if they are not already installed.
-
- 2. GUI Application Opens:
- A GUI window titled "iGEM SVCE-CHENNAI 23" should open if you click on the 'run'. This window contains the following elements:
-
- A label "Enter Sequence."
- An input field for entering a DNA sequence.
- A "FIND" button to start the analysis.
- A "CLEAR ENTRY" button to clear the input field.
- </p>
- <img src="https://static.igem.wiki/teams/4864/wiki/software/1.png" alt="P1">
+ <p>2. GUI Application Opens:</p>
+ <p>A GUI window titled "iGEM SVCE-CHENNAI 23" should open if you click on the 'run'. This window contains the following elements:</p>
+ <br>
+ <p>A label "Enter Sequence."<br>
+ An input field for entering a DNA sequence.<br>
+ A "FIND" button to start the analysis.<br>
+ A "CLEAR ENTRY" button to clear the input field.<br>
+ </p
+ <img src="https://static.igem.wiki/teams/4864/wiki/software/1.png" alt="P1" style="width: 50%; height: auto;">
</section>
<section class="desc-section">
- <p>3. Enter DNA Sequence:
+ <p>3. Enter DNA Sequence:<br>
Enter the DNA 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.
</p>
- <img src="https://static.igem.wiki/teams/4864/wiki/software/2.png" alt="P2">
+ <img src="https://static.igem.wiki/teams/4864/wiki/software/2.png" alt="P2" style="width: 50%; height: auto;">
</section>
<section class="desc-section">
- <p>4. Click "FIND":
+ <p>4. Click "FIND":<br>
After entering the DNA sequence, click the "FIND" button to initiate the analysis.
</p>
- <img src="https://static.igem.wiki/teams/4864/wiki/software/3.png" alt="P3">
+ <img src="https://static.igem.wiki/teams/4864/wiki/software/3.png" alt="P3" style="width: 50%; height: auto;">
</section>
<section class="desc-section">
- <p>5. Output:
+ <p>5. Output:<br>
The program will analyze the DNA sequence for the presence of an RBS (Ribosome Binding Site) in both the forward and reverse directions. The analysis includes the following information:
-
+ <br>
If an RBS is found in the forward direction:
-
- The position of the RBS
- The RBS sequence
- The position of the start codon (ATG)
- The length of the flanking region
- The flanking region sequence
- A message indicating whether the flanking region is ideal (between 5-7 nucleotides) or not.
-
+ <br>
+ The position of the RBS<br>
+ The RBS sequence<br>
+ The position of the start codon (ATG)<br>
+ The length of the flanking region<br>
+ The flanking region sequence<br>
+ A message indicating whether the flanking region is ideal (between 5-7 nucleotides) or not.<br>
</p>
- <img src="https://static.igem.wiki/teams/4864/wiki/software/4.png" alt="P4">
+ <img src="https://static.igem.wiki/teams/4864/wiki/software/4.png" alt="P4" style="width: 50%; height: auto;">
</section>
<section class="desc-section">
<p>If no RBS is found in the forward direction, it will display a message indicating that “NO RBS SEQUENCE FOUND IN FORWARD DIRECTIONâ€
-
+ <br>
If an RBS is found in the reverse direction:
-
+ <br>
It will show the same messages as the forward direction.
-
+ <br>
</p>
- <img src="https://static.igem.wiki/teams/4864/wiki/software/5.png" alt="P5">
+ <img src="https://static.igem.wiki/teams/4864/wiki/software/5.png" alt="P5" style="width: 50%; height: auto;">
</section>
</section>