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. If you are editing this page, please try to keep the tools in alphabectial order, by tool name.

Contents

DNA Tools

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

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

  • Colibri by Institut Pasteur
    • 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.
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