Team:XMU Software/Project protein/Example of optimization

From 2013.igem.org

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<div id="xmu_software_Example_of_optimization">
<div id="xmu_software_Example_of_optimization">
<div id="xmu_software_right_matrix"></div>
<div id="xmu_software_right_matrix"></div>
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<p>Example of optimization</p>
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</br><p>Example of optimization</p>
<table cellspacing="0" width="800" border="1" class="protein_table2">
<table cellspacing="0" width="800" border="1" class="protein_table2">
  <tr>
  <tr>
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  <tr>
  <tr>
<td>sequence input</td>
<td>sequence input</td>
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<td colspan="3">atggcttcctccgaagacgttatcaaagagttcatgcgtttcaaag
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<td colspan="3">
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  atggcttcctccgaagacgttatcaaagagttcatgcgtttcaaag
  ttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaagg
  ttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaagg
  tgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactg
  tgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactg
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  acatcacctcccacaacgaagactacaccatcgttgaacagtacga
  acatcacctcccacaacgaagactacaccatcgttgaacagtacga
  acgtgctgaaggtcgtcactccaccggtgcttaataacgctgatag
  acgtgctgaaggtcgtcactccaccggtgcttaataacgctgatag
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  <br/>tgctagtgtagatcgc</td>
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  tgctagtgtagatcgc</td>
  </tr>
  </tr>
  <tr>
  <tr>
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<td width="118"  height="212">sequence output</td>
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<td width="118">sequence output</td>
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<td colspan="3">ATGGCCAGCAGCGAGGACGTCATCAAGGAGTTCATGAGGTTTAAGG
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<td colspan="3">
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  ATGGCCAGCAGCGAGGACGTCATCAAGGAGTTCATGAGGTTTAAGG
  TCCGCATGGAGGGTTCGGTCAACGGTCATGAATTCGAGATCGAGGG
  TCCGCATGGAGGGTTCGGTCAACGGTCATGAATTCGAGATCGAGGG
  TGAAGGCGAGGGCCGCCCGTACGAAGGTACCCAGACCGCTAAGCTC
  TGAAGGCGAGGGCCGCCCGTACGAAGGTACCCAGACCGCTAAGCTC
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  AAGCCTGTGCAACTACCCGGTGCTTATAAGACGGACATCAAGCTTG
  AAGCCTGTGCAACTACCCGGTGCTTATAAGACGGACATCAAGCTTG
  ACATTACCTCCCACAATGAAGACTACACTATCGTCGAACAATATGA
  ACATTACCTCCCACAATGAAGACTACACTATCGTCGAACAATATGA
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  GCGTGCTGAGGGCAGGCACTCTACCGGTGCTTAGTAGCGGTAATGATGCTAGTGCAGGTCT</td>
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  GCGTGCTGAGGGCAGGCACTCTACCGGTGCTTAGTAGCGGTAATGA
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  <br />TGCTAGTGCAGGTCT</td>
  </tr>
  </tr>
  <tr>
  <tr>
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<td align="center">0.01 </td>
<td align="center">0.01 </td>
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  </tr>
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</table>
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</table></br></br></br> </br></br></br></br></br></br>
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Latest revision as of 02:12, 29 October 2013

<!DOCTYPE HTML>


Example of optimization

  RFP sequence
biobrick number E1010
sequence input atggcttcctccgaagacgttatcaaagagttcatgcgtttcaaag ttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaagg tgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactg aaagttaccaaaggtggtccgctgccgttcgcttgggacatcctgt ccccgcagttccagtacggttccaaagcttacgttaaacacccggc tgacatcccggactacctgaaactgtccttcccggaaggtttcaaa tgggaacgtgttatgaacttcgaagacggtggtgttgttaccgtta cccaggactcctccctgcaagacggtgagttcatctacaaagttaa actgcgtggtaccaacttcccgtccgacggtccggttatgcagaaa aaaaccatgggttgggaagcttccaccgaacgtatgtacccggaag acggtgctctgaaaggtgaaatcaaaatgcgtctgaaactgaaaga cggtggtcactacgacgctgaagttaaaaccacctacatggctaaa aaaccggttcagctgccgggtgcttacaaaaccgacatcaaactgg acatcacctcccacaacgaagactacaccatcgttgaacagtacga acgtgctgaaggtcgtcactccaccggtgcttaataacgctgatag tgctagtgtagatcgc
sequence output ATGGCCAGCAGCGAGGACGTCATCAAGGAGTTCATGAGGTTTAAGG TCCGCATGGAGGGTTCGGTCAACGGTCATGAATTCGAGATCGAGGG TGAAGGCGAGGGCCGCCCGTACGAAGGTACCCAGACCGCTAAGCTC AAAGTGACGAAGGGAGGGCCATTGCCCTTCGCCTGGGATATTCTCT CTCCCCAGTTCCAGTACGGAAGCAAAGCTTATGTCAAACACCCTGC TGACATTCCTGACTACTTGAAACTATCCTTCCCCGAGGGTTTCAAA TGGGAACGGGTCATGAACTTTGAAGACGGTGGCGTTGTTACTGTTA CCCAGGACTCGTCATTGCAGGACGGTGAATTTATCTACAAGGTCAA ACTACGTGGAACCAACTTCCCCTCCGATGGCCCTGTTATGCAGAAG AAGACTATGGGTTGGGAGGCTTCCACTGAGCGCATGTACCCTGAAG ATGGTGCCCTCAAGGGCGAAATAAAAATGCGCCTAAAGCTTAAAGA CGGCGGCCACTACGATGCTGAGGTTAAAACTACATACATGGCCAAG AAGCCTGTGCAACTACCCGGTGCTTATAAGACGGACATCAAGCTTG ACATTACCTCCCACAATGAAGACTACACTATCGTCGAACAATATGA GCGTGCTGAGGGCAGGCACTCTACCGGTGCTTAGTAGCGGTAATGA
TGCTAGTGCAGGTCT
protected enzyme cutting site ApaI
GGGCCC		 BamHI
GGATCC		 Bg1II
AGATCT

codon original numbers original proportion final numbers final proportion
AAA 22 0.09 9 0.04
AAC 4 0.02 3 0.01
AAG 0 0.00 13 0.06
AAT 0 0.00 1 0.00
ACA 0 0.00 1 0.00
ACC 14 0.06 6 0.03
ACG 0 0.00 2 0.01
ACT 0 0.00 5 0.02
AGA 1 0.00 0 0.00
AGC 0 0.00 3 0.01
AGG 0 0.00 3 0.01
AGT 0 0.00 0 0.00
ATA 0 0.00 1 0.00
ATC 9 0.04 5 0.02
ATG 9 0.04 9 0.04
ATT 0 0.00 3 0.01
CAA 1 0.00 2 0.01
CAC 5 0.02 4 0.02
CAG 7 0.03 6 0.03
CAT 0 0.00 1 0.00
CCA 0 0.00 1 0.00
CCC 0 0.00 5 0.02
CCG 12 0.05 1 0.00
CCT 0 0.00 5 0.02
CGA 0 0.00 0 0.00
CGC 1 0.00 4 0.02
CGG 0 0.00 2 0.01
CGT 9 0.04 2 0.01
CTA 0 0.00 4 0.02
CTC 0 0.00 3 0.01
CTG 12 0.05 0 0.00
CTT 0 0.00 2 0.01
GAA 19 0.08 10 0.04
GAC 14 0.06 10 0.04
GAG 3 0.01 12 0.05
GAT 0 0.00 4 0.02
GCA 0 0.00 0 0.00
GCC 0 0.00 4 0.02
GCG 0 0.00 0 0.00
GCT 12 0.05 8 0.03
GGA 0 0.00 3 0.01
GGC 0 0.00 8 0.03
GGG 0 0.00 1 0.00
GGT 23 0.10 11 0.05
GTA 0 0.00 0 0.00
GTC 0 0.00 7 0.03
GTG 0 0.00 2 0.01
GTT 14 0.06 5 0.02
TAA 2 0.01 1 0.00
TAC 11 0.05 8 0.03
TAG 2 0.01 3 0.01
TAT 0 0.00 3 0.01
TCA 0 0.00 1 0.00
TCC 12 0.05 4 0.02
TCG 1 0.00 2 0.01
TCT 0 0.00 3 0.01
TGA 1 0.00 1 0.00
TGC 1 0.00 2 0.01
TGG 3 0.01 3 0.01
TGT 1 0.00 0 0.00
TTA 0 0.00 0 0.00
TTC 10 0.04 7 0.03
TTG 0 0.00 3 0.01
TTT 0 0.00 3 0.01









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