Synthetic Biology:Tools

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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.
  • 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.