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Team:XMU Software/Project protein/Example of optimization
From 2013.igem.org
(Difference between revisions)
| Line 20: | Line 20: | ||
<tr> | <tr> | ||
<td>sequence input</td> | <td>sequence input</td> | ||
| - | <td colspan="3">atggcttcctccgaagacgttatcaaagagttcatgcgtttcaaag | + | <td colspan="3"> |
| + | atggcttcctccgaagacgttatcaaagagttcatgcgtttcaaag | ||
ttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaagg | ttcgtatggaaggttccgttaacggtcacgagttcgaaatcgaagg | ||
tgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactg | tgaaggtgaaggtcgtccgtacgaaggtacccagaccgctaaactg | ||
| Line 33: | Line 34: | ||
cggtggtcactacgacgctgaagttaaaaccacctacatggctaaa | cggtggtcactacgacgctgaagttaaaaccacctacatggctaaa | ||
aaaccggttcagctgccgggtgcttacaaaaccgacatcaaactgg | aaaccggttcagctgccgggtgcttacaaaaccgacatcaaactgg | ||
| - | + | acatcacctcccacaacgaagactacaccatcgttgaacagtacga | |
| + | acgtgctgaaggtcgtcactccaccggtgcttaataacgctgatag | ||
| + | tgctagtgtagatcgc</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td width="118">sequence output</td> | <td width="118">sequence output</td> | ||
| - | <td colspan="3">ATGGCCAGCAGCGAGGACGTCATCAAGGAGTTCATGAGGTTTAAGG | + | <td colspan="3"> |
| + | ATGGCCAGCAGCGAGGACGTCATCAAGGAGTTCATGAGGTTTAAGG | ||
TCCGCATGGAGGGTTCGGTCAACGGTCATGAATTCGAGATCGAGGG | TCCGCATGGAGGGTTCGGTCAACGGTCATGAATTCGAGATCGAGGG | ||
TGAAGGCGAGGGCCGCCCGTACGAAGGTACCCAGACCGCTAAGCTC | TGAAGGCGAGGGCCGCCCGTACGAAGGTACCCAGACCGCTAAGCTC | ||
| Line 51: | Line 55: | ||
AAGCCTGTGCAACTACCCGGTGCTTATAAGACGGACATCAAGCTTG | AAGCCTGTGCAACTACCCGGTGCTTATAAGACGGACATCAAGCTTG | ||
ACATTACCTCCCACAATGAAGACTACACTATCGTCGAACAATATGA | ACATTACCTCCCACAATGAAGACTACACTATCGTCGAACAATATGA | ||
| - | + | GCGTGCTGAGGGCAGGCACTCTACCGGTGCTTAGTAGCGGTAATGA | |
| + | TGCTAGTGCAGGTCT</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
Revision as of 02:10, 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 |
