Difference between revisions of "Team:NEFU China/Software1"

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<section id="resume" style="box-shadow: inset 0px 15px 15px -15px green">
 
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<div class="row introduction" >
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<div class="row introduction">
 
<div class="three columns header-col">
 
<div class="three columns header-col">
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             <h1><span>intorduction</span></h1>
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             <h1><span style="
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    color: orange;
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">introduce</span></h1>
 
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         <div class="nine columns main-col">
 
         <div class="nine columns main-col">
 
             <div class="row item">
 
             <div class="row item">
 
<div class="twelve columns">
 
<div class="twelve columns">
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<h3>Aim</h3>
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<h3 style="
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">Aim</h3>
 
<p class="info">Build Coding Book</p>
 
<p class="info">Build Coding Book</p>
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<p>
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<p style="
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    font-size: 26px!important;
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">
 
In English text, each letter has a certain frequency. We constructed a list of letter frequencies for each letter. Also, in living organisms, each codon is used with a certain frequency. Based on this relationship between English letters and codons,  we find out the correspondence between letters and codons by using DFS (Depth First Search) algorithm and optimization arithmetic.
 
In English text, each letter has a certain frequency. We constructed a list of letter frequencies for each letter. Also, in living organisms, each codon is used with a certain frequency. Based on this relationship between English letters and codons,  we find out the correspondence between letters and codons by using DFS (Depth First Search) algorithm and optimization arithmetic.
 
</p>
 
</p>
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  <h3>Programming</h3>
 
  <h3>Programming</h3>
 
      <br>
 
      <br>
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  <p>
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  <p style="
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    font-size: 26px!important;
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">
 
      <strong>1. Create a letter-frequency table and a codon-frequency table.</strong><br>
 
      <strong>1. Create a letter-frequency table and a codon-frequency table.</strong><br>
 
  According to the literature, we obtain the information of the frequency of letters and codons.
 
  According to the literature, we obtain the information of the frequency of letters and codons.
 
  <br><br>
 
  <br><br>
 
  <strong>2. Find out the correspondence between letters and codons by using DFS Algorithm.</strong><br>
 
  <strong>2. Find out the correspondence between letters and codons by using DFS Algorithm.</strong><br>
−
  We build up a tree structure where the codons and the frequency of the codons are stored on each node. Then we use the depth-first search algorithm to traverse down from the root node successively, and match condon-frequence with the letter- frequency to obtain the correspondence between letters and codons.<br>
+
  We build up a tree structure where the codons and the frequency of the codons are stored on each node. Then we use the depth-first search algorithm to traverse down from the root node successively, and match condon-frequence with the letter- frequency to obtain the correspondence between letters and codons.
 +
<br><br>
 
                       The tree structure is shown in the figure 1.<br>
 
                       The tree structure is shown in the figure 1.<br>
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  <img style="width:750px;" src="https://static.igem.org/mediawiki/2018/b/bd/T--NEFU_China--software1-tree.png"><br>
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  <div align="center">
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<img style="width:750px;" src="https://static.igem.org/mediawiki/2018/b/bd/T--NEFU_China--software1-tree.png"><br>
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</div>
 
  Figure 1. Tree Structute.
 
  Figure 1. Tree Structute.
 
      <br><br>
 
      <br><br>
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  <strong>3. Get the optimal solution by using optional algorithm.</strong><br>
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  <p style="
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    font-size: 26px!important;
 +
">
 +
    <strong>3. Get the optimal solution by using optional algorithm.</strong></p>
 
  In step 2, we get the correspondence between letters and codons. But some letters have multiple corresponding relationships. For example, in figure 1, the letters E and T correspond to codons GAU, GCU, GAA, E and T also correspond to codons GAU, GCU, AUG. What’s more, the letter T can also correspond to codons GAU, GCU, GCA. Therefore, we use the optimal algorithm to determine one of the multiple correspondence. <br>  
 
  In step 2, we get the correspondence between letters and codons. But some letters have multiple corresponding relationships. For example, in figure 1, the letters E and T correspond to codons GAU, GCU, GAA, E and T also correspond to codons GAU, GCU, AUG. What’s more, the letter T can also correspond to codons GAU, GCU, GCA. Therefore, we use the optimal algorithm to determine one of the multiple correspondence. <br>  
 
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       <div class="row results">
 
       <div class="row results">
 
         <div class="three columns header-col">
 
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             <h1><span>RESULTS</span></h1>
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             <h1><span style="
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">RESULTS</span></h1>
 
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         <div class="nine columns main-col">
 
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               <div class="twelve columns">
 
               <div class="twelve columns">
 
               <h3>Print the correspondence between letters and codons</h3>
 
               <h3>Print the correspondence between letters and codons</h3>
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                   <p style="
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Output:<br>
 
Output:<br>
 
<br>
 
<br>
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  <div class="row others">
 
  <div class="row others">
 
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             <h1><span>Others</span></h1>
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             <h1><span style="
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">Others</span></h1>
 
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         <div class="nine columns main-col" style="
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               <h3>Visual Software</h3>
 
               <h3>Visual Software</h3>
 
                  
 
                  
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">
 
                   We developed a visual software. There are an input textbox, an output textbox, two radio buttons and a translate button in the software interface. We can choose radio buttons to select letters to codons or codons to letters. In addition to these, our software can also provide open files, copy files, cut files, save files, print files and other basic functions.<br>
 
                   We developed a visual software. There are an input textbox, an output textbox, two radio buttons and a translate button in the software interface. We can choose radio buttons to select letters to codons or codons to letters. In addition to these, our software can also provide open files, copy files, cut files, save files, print files and other basic functions.<br>
 
      Software interface:<br>
 
      Software interface:<br>
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      <img style="width:750px;" src="https://static.igem.org/mediawiki/2018/5/5c/T--NEFU_China--software-v1.png">
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      <br>
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<div align="center">
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<img style="width:750px;" src="https://static.igem.org/mediawiki/2018/5/5c/T--NEFU_China--software-v1.png"><br>
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</div>
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<br>
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      Letters to Codons:<br>
 
      Letters to Codons:<br>
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  <img style="width:750px;" src="https://static.igem.org/mediawiki/2018/3/35/T--NEFU_China--software-v2.png">
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  <div align="center">
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<img style="width:750px;" src="https://static.igem.org/mediawiki/2018/3/35/T--NEFU_China--software-v2.png">
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</div><br>
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  Codons to letters:<br>
 
  Codons to letters:<br>
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  <img style="width:750px;" src="https://static.igem.org/mediawiki/2018/8/8d/T--NEFU_China--software-v3.png">
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  <div align="center">
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<img style="width:750px;" src="https://static.igem.org/mediawiki/2018/8/8d/T--NEFU_China--software-v3.png">
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<div></div></div>
 
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</body>
 
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</html>
 
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Revision as of 02:25, 18 October 2018

Software 1

introduce

Aim

Build Coding Book

In English text, each letter has a certain frequency. We constructed a list of letter frequencies for each letter. Also, in living organisms, each codon is used with a certain frequency. Based on this relationship between English letters and codons, we find out the correspondence between letters and codons by using DFS (Depth First Search) algorithm and optimization arithmetic.

Programming


1. Create a letter-frequency table and a codon-frequency table.
According to the literature, we obtain the information of the frequency of letters and codons.

2. Find out the correspondence between letters and codons by using DFS Algorithm.
We build up a tree structure where the codons and the frequency of the codons are stored on each node. Then we use the depth-first search algorithm to traverse down from the root node successively, and match condon-frequence with the letter- frequency to obtain the correspondence between letters and codons.

The tree structure is shown in the figure 1.


Figure 1. Tree Structute.

3. Get the optimal solution by using optional algorithm.

In step 2, we get the correspondence between letters and codons. But some letters have multiple corresponding relationships. For example, in figure 1, the letters E and T correspond to codons GAU, GCU, GAA, E and T also correspond to codons GAU, GCU, AUG. What’s more, the letter T can also correspond to codons GAU, GCU, GCA. Therefore, we use the optimal algorithm to determine one of the multiple correspondence.

RESULTS

Print the correspondence between letters and codons

Output:

Draw letter-frequency histogram

Others

Visual Software

We developed a visual software. There are an input textbox, an output textbox, two radio buttons and a translate button in the software interface. We can choose radio buttons to select letters to codons or codons to letters. In addition to these, our software can also provide open files, copy files, cut files, save files, print files and other basic functions.
Software interface:



Letters to Codons:

Codons to letters:

Download

1.Coding 2.Visualization 3.Visualizaiton.exe