Synthetic Biology:Tools

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.

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

• Appendix by Ambion, Inc.
  • Website with many useful nucleic acid parameters.

• 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.

Protein Tools

• ExPASy Proteomics server by the Swiss Institute of Bioinformatics
  • Collection of links to many pages to calculate parameters of your favorite proteins

• Zinc Finger Tools by Barbas Lab
  • Design Zinc Finger DNA binding proteins

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.

• Registry of Standard Biological Parts by MIT
  • Open repository of BioBricks; the place for all your standard biological parts.