Synthetic Biology:Tools

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(DNA Tools)
(DNA Tools)
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*[http://www.dna20.com/commerce/customer/emailsupp.jsp GeneDesigner] by DNA2.0
*[http://www.dna20.com/commerce/customer/emailsupp.jsp 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.
**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.
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**Free to download and works on Mac or PC.  User agreement is somewhat restrictive.
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**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).
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] by New England Biolabs, Inc.
*[http://tools.neb.com/NEBcutter2/index.php NEB Cutter] by New England Biolabs, Inc.

Revision as of 23:06, 20 June 2006

Go to http://syntheticbiology.org/

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. If you are editing this page, please try to keep the tools in alphabetical 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
  • 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.
  • 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.

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.

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