Synthetic Biology:Tools

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Synthetic Biology is
A) the design and construction of new biological parts, devices, and systems, and
B) the re-design of existing, natural biological systems for useful purposes.

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This page contains a collection of links to online tools that are related to Synthetic Biology. <wikionly>If you are editing this page, please try to keep the tools in alphabetical order, by tool name.</wikionly>

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

• Clipboard by Austin Che
  • Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence

• File format converter by Austin Che
  • Web tool for converting between sequence file formats.

• Gene Design by Boeke lab
  • Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.

• GeneDesigner by DNA2.0
  • Combine genetic building blocks by drag-and-drop, codon optimize, restriction site editing, sequence oligo design etc. See BMC Bioinformatics 2006 Jun 6;7(1):285 for more detail.
  • Free to download and works on Mac or PC. User agreement is somewhat restrictive (i.e., does not allow commercial application to anything designed on the program).

• 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.

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

• 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

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.

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Making life better, one part at a time.