This page contains 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 alphabetical order, by tool name.
- 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
- Clipboard by Austin Che
- Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence
- 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 tool for sequence analysis and data management.
- 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.
- Cn3D by NCBI
- A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. It doesn't read PDB files but can be more straightforward to use than DeepView.
- DeepView by GlaxoSmithKline & Swiss Institute of Bioinformatics
- Awesome program for viewing and studying protein structure.
- ExPASy Proteomics server by the Swiss Institute of Bioinformatics
- Collection of links to many pages to calculate parameters of your favorite proteins
- Modeller by Sali Lab
- For homology or comparative modeling of protein three-dimensional structures.
- Zinc Finger Tools by Barbas Lab
- Design Zinc Finger DNA binding proteins
- 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.
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