Team:XMU Software/Project protein/Example of optimization

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				</br><p>Example of optimization</p>
				<table cellspacing="0" width="800" border="1" class="protein_table2">
				  <tr>
					<td>&nbsp;</td>
					<td colspan="3" width="622">RFP sequence</td>
				  </tr>
				  <tr>
					<td>biobrick number</td>
					<td colspan="3">E1010</td>
				  </tr>
				  <tr>
					<td>sequence input</td>
					<td colspan="3">
					   atggcttcctccgaagacgttatcaaagagttcatgcgtttcaaag
					   ttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaagg
					   tgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactg
					   aaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgt
					   ccccgcagttccagtacggttccaaagcttacgttaaacacccggc
					   tgacatcccggactacctgaaactgtccttcccggaaggtttcaaa
					   tgggaacgtgttatgaacttcgaagacggtggtgttgttaccgtta
					   cccaggactcctccctgcaagacggtgagttcatctacaaagttaa
					   actgcgtggtaccaacttcccgtccgacggtccggttatgcagaaa
					   aaaaccatgggttgggaagcttccaccgaacgtatgtacccggaag
					   acggtgctctgaaaggtgaaatcaaaatgcgtctgaaactgaaaga
					   cggtggtcactacgacgctgaagttaaaaccacctacatggctaaa
					   aaaccggttcagctgccgggtgcttacaaaaccgacatcaaactgg
					   acatcacctcccacaacgaagactacaccatcgttgaacagtacga
					   acgtgctgaaggtcgtcactccaccggtgcttaataacgctgatag
					   tgctagtgtagatcgc</td>
				  </tr>
				  <tr>
					<td width="118">sequence output</td>
					<td colspan="3">
					   ATGGCCAGCAGCGAGGACGTCATCAAGGAGTTCATGAGGTTTAAGG
					   TCCGCATGGAGGGTTCGGTCAACGGTCATGAATTCGAGATCGAGGG
					   TGAAGGCGAGGGCCGCCCGTACGAAGGTACCCAGACCGCTAAGCTC
					   AAAGTGACGAAGGGAGGGCCATTGCCCTTCGCCTGGGATATTCTCT
					   CTCCCCAGTTCCAGTACGGAAGCAAAGCTTATGTCAAACACCCTGC
					   TGACATTCCTGACTACTTGAAACTATCCTTCCCCGAGGGTTTCAAA
					   TGGGAACGGGTCATGAACTTTGAAGACGGTGGCGTTGTTACTGTTA
					   CCCAGGACTCGTCATTGCAGGACGGTGAATTTATCTACAAGGTCAA
					   ACTACGTGGAACCAACTTCCCCTCCGATGGCCCTGTTATGCAGAAG
					   AAGACTATGGGTTGGGAGGCTTCCACTGAGCGCATGTACCCTGAAG
					   ATGGTGCCCTCAAGGGCGAAATAAAAATGCGCCTAAAGCTTAAAGA
					   CGGCGGCCACTACGATGCTGAGGTTAAAACTACATACATGGCCAAG
					   AAGCCTGTGCAACTACCCGGTGCTTATAAGACGGACATCAAGCTTG
					   ACATTACCTCCCACAATGAAGACTACACTATCGTCGAACAATATGA
					   GCGTGCTGAGGGCAGGCACTCTACCGGTGCTTAGTAGCGGTAATGA
					   TGCTAGTGCAGGTCT</td>
				  </tr>
				  <tr>
					<td width="118">protected enzyme cutting site</td>

					
						<td width="118">ApaI<br />
						  GGGCCC</td>
						<td width="118">BamHI<br />
						  GGATCC</td>
						<td width="118">Bg1II<br />
						  AGATCT</td>

				  </tr>
				</table>	
			<br/>
			<table cellspacing="0" class="protein_table2" border="1" width="800">
			  <col width="82" />
			  <col width="134" />
			  <col width="104" />
			  <col width="88" />
			  <col width="87" />
			  <tr>
				<td width="82">codon</td>
				<td width="134">original numbers</td>
				<td width="104">original proportion</td>
				<td width="88">final numbers</td>
				<td width="87">final proportion</td>
			  </tr>
			  <tr>
				<td>AAA</td>
				<td align="center">22</td>
				<td align="center">0.09 </td>
				<td align="center">9</td>
				<td align="center">0.04 </td>
			  </tr>
			  <tr>
				<td>AAC</td>
				<td align="center">4</td>
				<td align="center">0.02 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>AAG</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">13</td>
				<td align="center">0.06 </td>
			  </tr>
			  <tr>
				<td>AAT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>ACA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>ACC</td>
				<td align="center">14</td>
				<td align="center">0.06 </td>
				<td align="center">6</td>
				<td align="center">0.03 </td>
			  </tr>
			  <tr>
				<td>ACG</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>ACT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">5</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>AGA</td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>AGC</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>AGG</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>AGT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>ATA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>ATC</td>
				<td align="center">9</td>
				<td align="center">0.04 </td>
				<td align="center">5</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>ATG</td>
				<td align="center">9</td>
				<td align="center">0.04 </td>
				<td align="center">9</td>
				<td align="center">0.04 </td>
			  </tr>
			  <tr>
				<td>ATT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>CAA</td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>CAC</td>
				<td align="center">5</td>
				<td align="center">0.02 </td>
				<td align="center">4</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>CAG</td>
				<td align="center">7</td>
				<td align="center">0.03 </td>
				<td align="center">6</td>
				<td align="center">0.03 </td>
			  </tr>
			  <tr>
				<td>CAT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>CCA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>CCC</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">5</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>CCG</td>
				<td align="center">12</td>
				<td align="center">0.05 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>CCT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">5</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>CGA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>CGC</td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
				<td align="center">4</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>CGG</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>CGT</td>
				<td align="center">9</td>
				<td align="center">0.04 </td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>CTA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">4</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>CTC</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>CTG</td>
				<td align="center">12</td>
				<td align="center">0.05 </td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>CTT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>GAA</td>
				<td align="center">19</td>
				<td align="center">0.08 </td>
				<td align="center">10</td>
				<td align="center">0.04 </td>
			  </tr>
			  <tr>
				<td>GAC</td>
				<td align="center">14</td>
				<td align="center">0.06 </td>
				<td align="center">10</td>
				<td align="center">0.04 </td>
			  </tr>
			  <tr>
				<td>GAG</td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
				<td align="center">12</td>
				<td align="center">0.05 </td>
			  </tr>
			  <tr>
				<td>GAT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">4</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>GCA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>GCC</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">4</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>GCG</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>GCT</td>
				<td align="center">12</td>
				<td align="center">0.05 </td>
				<td align="center">8</td>
				<td align="center">0.03 </td>
			  </tr>
			  <tr>
				<td>GGA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>GGC</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">8</td>
				<td align="center">0.03 </td>
			  </tr>
			  <tr>
				<td>GGG</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>GGT</td>
				<td align="center">23</td>
				<td align="center">0.10 </td>
				<td align="center">11</td>
				<td align="center">0.05 </td>
			  </tr>
			  <tr>
				<td>GTA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>GTC</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">7</td>
				<td align="center">0.03 </td>
			  </tr>
			  <tr>
				<td>GTG</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>GTT</td>
				<td align="center">14</td>
				<td align="center">0.06 </td>
				<td align="center">5</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>TAA</td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>TAC</td>
				<td align="center">11</td>
				<td align="center">0.05 </td>
				<td align="center">8</td>
				<td align="center">0.03 </td>
			  </tr>
			  <tr>
				<td>TAG</td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>TAT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>TCA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>TCC</td>
				<td align="center">12</td>
				<td align="center">0.05 </td>
				<td align="center">4</td>
				<td align="center">0.02 </td>
			  </tr>
			  <tr>
				<td>TCG</td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>TCT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>TGA</td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>TGC</td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
				<td align="center">2</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>TGG</td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>TGT</td>
				<td align="center">1</td>
				<td align="center">0.00 </td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>TTA</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
			  </tr>
			  <tr>
				<td>TTC</td>
				<td align="center">10</td>
				<td align="center">0.04 </td>
				<td align="center">7</td>
				<td align="center">0.03 </td>
			  </tr>
			  <tr>
				<td>TTG</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			  <tr>
				<td>TTT</td>
				<td align="center">0</td>
				<td align="center">0.00 </td>
				<td align="center">3</td>
				<td align="center">0.01 </td>
			  </tr>
			</table></br></br></br>	</br></br></br></br></br></br>									
			
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				$(".right-menu").mouseover(function(){
					$("#search-controls").show();
					$(".right-menu").show();
					$("#mw-searchButton").show();
					$("#searchGoButton").show();
				});
				 $("#xmu_software_right_matrix").mouseout(function(){
					$("#search-controls").hide();
					$(".right-menu").hide();
					$("#mw-searchButton").hide();
					$("#searchGoButton").hide();
				});
				if($(".left-menu").find("li").size()==7)
				{
					$(".left-menu").find("li").eq(6).html("");  
					$("#menubar").get(0).style.width="330px";
				}
				else
				{
					$(".left-menu").find("li").eq(4).html("");  
					$("#menubar").get(0).style.width="280px";	
					$("#pt-login").get(0).style.right="50px";
				}
				$("#xmu_body").scroll(function(){
					$("#search-controls").hide();
					$(".right-menu").hide();
					$("#mw-searchButton").hide();
					$("#searchGoButton").hide();
				});
		</script>			
	</body>
</html>