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Synthetic Biology:Tools: Difference between revisions
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===DNA Tools=== | ===DNA Tools=== | ||
*[http://alpha.dmi.unict.it/~ctnyu/bbocus.html BBOCUS] by Ferro and Purrello lab | |||
**BBOCUS (BackTranslation Based On Codon Usage Strategy) is a re-implementation of the algorithm in Graziano Pesole's BACKTR. It's based on cluster analysis (Complete Linkage algorithm), that requires a similarity matrix D containing distance between each pair of sequences of mRNA. After cluster analysis, backtranslation is performed on sequences of homogeneous pool. Unlike in Graziano Pesole's method, where the choose of homogeneous pool was made by a biologist, the choose of cluster in BBOCUS is fully automatic. A Codon Usage Table (CUT) is created through sequences of homogeneuos pool. Generally, to backtranslate an amino acid in a protein the codon chosen it is the one has maximum frequency. | |||
*[http://paris.chem.yale.edu/extinct.html Biopolymer calculator] by Schepartz lab | *[http://paris.chem.yale.edu/extinct.html Biopolymer calculator] by Schepartz lab | ||
**Calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein | **Calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein | ||
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*[http://synbio.mit.edu/tools/clipboard.cgi Clipboard] by [[Austin Che]] | *[http://synbio.mit.edu/tools/clipboard.cgi Clipboard] by [[Austin Che]] | ||
**Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence | **Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence | ||
*[http://helixweb.nih.gov/dnaworks/ DNAWorks] by Hoover and Lubkowski | |||
**A web tool for optimizing melting temperature during gene synthesis. | |||
*[http://synbio.mit.edu/tools/converter.cgi File format converter] by [[Austin Che]] | *[http://synbio.mit.edu/tools/converter.cgi File format converter] by [[Austin Che]] | ||
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*[http://www.evolvingcode.net/codon/sgd/index.php Synthetic Gene Designer] by Gang Wu | *[http://www.evolvingcode.net/codon/sgd/index.php Synthetic Gene Designer] by Gang Wu | ||
**A web platform that allows codon optimization to various extent. | **A web platform that allows codon optimization to various extent. | ||
**Compatible with non-standard genetic | **Compatible with non-standard genetic codes | ||
**Integrate CUTG | **Integrate CUTG | ||
**Restriction site avoidance | **Restriction site avoidance | ||
