Difference between revisions of "Synthetic Biology:Tools"

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(DNA Tools)
(DNA Tools)
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*[http://slam.bs.jhmi.edu/gd/ Gene Design] by Boeke lab
 
*[http://slam.bs.jhmi.edu/gd/ Gene Design] by Boeke lab
 
**Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.
 
**Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.
 +
 
*[http://www.invitrogen.com/content.cfm?pageid=10373 Vector NTI] by Informax, Inc.
 
*[http://www.invitrogen.com/content.cfm?pageid=10373 Vector NTI] by Informax, Inc.
 +
**Free-to-academics Windows-only tool for sequence analysis and data management.
 +
 
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] by New England Biolabs, Inc.
 
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] by New England Biolabs, Inc.
**Tool for finding restriction sites, et cetera
+
**Tool for finding restriction sites, et cetera.
**Free-to-academics Windows-only tool for sequence analysis and data management.
+
 
 
*[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

Revision as of 18:35, 17 September 2005

Via this page, we hope to maintain a collection of links to online tools that are related to Synthetic Biology

DNA Tools

  • Gene Design by Boeke lab
    • Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.
  • Vector NTI by Informax, Inc.
    • Free-to-academics Windows-only tool for sequence analysis and data management.
  • NEB Cutter by New England Biolabs, Inc.
    • Tool for finding restriction sites, et cetera.
  • 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

RNA Tools

  • mFold by Michael Zuker. This is the main page with links to sites for predicting RNA and DNA folds, calculating Tm's and free energies.
  • Ambion's site with many useful nucleic acid parameters.

Protein Tools

General Tools

  • Registry of Standard Biological Parts
  • Colibri
    • E. coli genome site; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff. You can also search for protein sequences/motifs within the E. coli genome.