Synthetic Biology:Tools: Difference between revisions
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===General Tools=== | ===General Tools=== | ||
* [http://parts.mit.edu/ Registry of Standard Biological Parts] | * [http://parts.mit.edu/ Registry of Standard Biological Parts] | ||
*[http://genolist.pasteur.fr/Colibri/ 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. | *[http://genolist.pasteur.fr/Colibri/ 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. | |||
Revision as of 18:31, 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.
- 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
- Zinc Finger Tools by Barbas Lab
- Design Zinc Finger DNA binding proteins
- ExPASy Proteomics server
- Collection of links to many pages to calculate parameters of your favorite proteins
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.
