Team:StanfordBrownSpelman/Modelling
From 2014.igem.org
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- | == | + | <!-- ====== Project Header ====== --> |
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+ | <div class="row"> | ||
+ | <div class="small-5 small-centered columns projecticon-cellulose-acetate"><img class="projecticon-cellulose-acetate" src="https://static.igem.org/mediawiki/2014/c/c6/SBS_iGEM_2014_Hell_Cell.png"/> | ||
+ | </div> | ||
+ | <div id="header" class="small-8 small-centered columns"> | ||
+ | <h3><center><a href="https://2014.igem.org/Team:StanfordBrownSpelman/Modelling">Double Optimizer</a></h3> | ||
+ | <h7><center>A utility for simultaneous codon optimization and optimization for gene synthesis</h7> | ||
+ | <h6> | ||
+ | Gene synthesis as a tool for biological engineering presents both opportunities and challenges. One opportunity presented is the ability to optimize codon usage in a gene to match that of a host organism. Compared to traditional cloning methods, this can increase protein yields in the host organism by several fold. However, while there exist a large number of freely-usable programs that perform codon optimization, there is no guarantee that the sequences these programs provide will be able to be synthesized. Specifically, in the case of genes with repetitive amino acid sequences, these programs will often generate outputs that contain too many repeated short DNA sequences to be synthesized commercially. | ||
+ | <br></br> | ||
As an example, the hypothetical protein X777_06170 from the ant species ''Cerapachys biroi'' has an amino acid sequence that appears to be somewhat repetitive: | As an example, the hypothetical protein X777_06170 from the ant species ''Cerapachys biroi'' has an amino acid sequence that appears to be somewhat repetitive: | ||
- | 1 mklfkclvpv vvlllikdss arpglirdfv ggtvgsilep fqilkpkdsy adanshasah | + | <br></br> |
- | 61 nlggtfslgp vslggglssa sasssasang gglasasska daqaggygyg gsnanaqasa | + | 1 mklfkclvpv vvlllikdss arpglirdfv ggtvgsilep fqilkpkdsy adanshasah <br></br> |
- | 121 sanaqgggyg nggihgiypg qqgvhggnpf lggagsnana naiananaqa naggnngglg | + | 61 nlggtfslgp vslggglssa sasssasang gglasasska daqaggygyg gsnanaqasa <br></br> |
- | 181 syggyqqggn ypidsstgpi gnnpflsggh gdgnanaaan anagasaign gggpidvnnp | + | 121 sanaqgggyg nggihgiypg qqgvhggnpf lggagsnana naiananaqa naggnngglg <br></br> |
- | 241 flhggaansg agginyqpgn aggiilsekp lglptiypgq hppayldsig spgansnaga | + | 181 syggyqqggn ypidsstgpi gnnpflsggh gdgnanaaan anagasaign gggpidvnnp <br></br> |
- | 301 napcsecgss gatilgyegq glggikesgs sgatilgyeg qglggikesg ssgatilgye | + | 241 flhggaansg agginyqpgn aggiilsekp lglptiypgq hppayldsig spgansnaga <br></br> |
- | 361 gqglggikes gssgatilgs ydgqgpsgat ilgdyngqgl ggikessgvt vlgdyegqgl | + | 301 napcsecgss gatilgyegq glggikesgs sgatilgyeg qglggikesg ssgatilgye <br></br> |
- | 421 ggisgphggh gqaganagan ananagatvg ssggvlggvg dhggyhgyng hdgssglnlg | + | 361 gqglggikes gssgatilgs ydgqgpsgat ilgdyngqgl ggikessgvt vlgdyegqgl <br></br> |
- | 481 gygggsnana qassnalass ggsssatsda lsnahssggs alanssskas angsgsanan | + | 421 ggisgphggh gqaganagan ananagatvg ssggvlggvg dhggyhgyng hdgssglnlg <br></br> |
- | 541 ahassnassg shglgsktsa ssqasasadt rdmlifs | + | 481 gygggsnana qassnalass ggsssatsda lsnahssggs alanssskas angsgsanan <br></br> |
+ | 541 ahassnassg shglgsktsa ssqasasadt rdmlifs <br></br> | ||
Note that this sequence is not simply the same sequence repeated multiple times, but instead contains several motifs on the order of 10 - 20 amino acids in length that occur several times. When this sequence was run through the codon optimization program for expression in ''E. coli'' provided by a major DNA synthesis firm, the resulting output could not be synthesized by the very same firm: the "optimized" DNA sequence contained too many recurring short (> 8 nucleotide) DNA sequences to allow for synthesis. | Note that this sequence is not simply the same sequence repeated multiple times, but instead contains several motifs on the order of 10 - 20 amino acids in length that occur several times. When this sequence was run through the codon optimization program for expression in ''E. coli'' provided by a major DNA synthesis firm, the resulting output could not be synthesized by the very same firm: the "optimized" DNA sequence contained too many recurring short (> 8 nucleotide) DNA sequences to allow for synthesis. | ||
- | + | <br></br> | |
- | + | Manually correcting for repeats in the codon-optimized DNA sequence is a sub-optimal solution: not only is this process time-consuming, but it has the tendency to undo the codon-optimization: if a sequence of amino acids occurs several times, one may be forced to use all possible codon-combinations to represent this sequence to avoid nucleotide-sequence repetition. Unless corrected for by skewing codon usage elsewhere in the sequence, this will tend to make the codon usage more uniform than is optimal for the expression vector. Additionally, any changes made in either correcting for repeats or re-correcting for codon usage may in turn introduce additional repeats. | |
+ | <br></br> | ||
- | + | </h6> | |
+ | </div> | ||
+ | </div> | ||
+ | <!-- ====== Solution: Double Optimizer ====== --> | ||
- | + | <div class="row"> | |
+ | <div id="subheader" class="small-8 small-centered columns"> | ||
+ | <h5><center>Solution: Double Optimizer</h5> | ||
+ | <h6> | ||
+ | DoubleOptimizer is a software tool we have created to optimize codon usage in a gene both to match a given codon usage distribution and to avoid repetition of nucleotide sequences. Given a DNA or amino acid sequence and a desired codon distribution, DoubleOptimizer will produce, within a matter of minutes, an equivalent sequence that has substantially reduced DNA sequence repetition, while also closely matching the desired codon usage. | ||
+ | </h6> | ||
+ | </div> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <!-- ====== Solution: Double Optimizer ====== --> | ||
+ | |||
+ | <div class="row"> | ||
+ | <div id="subheader" class="small-8 small-centered columns"> | ||
+ | <h5><center>Availability and Usage</h5> | ||
+ | <h6> | ||
+ | DoubleOptimizer may be downloaded <a href = "https://drive.google.com/a/brown.edu/file/d/0B6Q5Eo65G4cPZC1SZWEzbUtrYUU/view?usp=sharing"> here </a>. | ||
- | + | <br></br> | |
DoubleOptimizer is a command line utility, provided as a Java jar file. It can be invoked from command line on any system with Java installed, with the following syntax: | DoubleOptimizer is a command line utility, provided as a Java jar file. It can be invoked from command line on any system with Java installed, with the following syntax: | ||
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This will cause the symbols X,*, and - to be ignored in the proteome. | This will cause the symbols X,*, and - to be ignored in the proteome. | ||
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+ | </h6> | ||
+ | </div> | ||
+ | </div> |
Revision as of 18:02, 10 October 2014