Synthetic Biology:Tools: Difference between revisions

Revision as of 18:30, 17 September 2005

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

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

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.

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

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.

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 ===DNA Tools===
-* [http://www.invitrogen.com/content.cfm?pageid=10373 Vector NTI] by Informax, Inc.
+*[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.
+*[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://paris.chem.yale.edu/extinct.html Biopolymer calculator] by Schepartz lab