Difference between revisions of "Synthetic Biology:Tools"

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*[http://slam.bs.jhmi.edu/gd/ Gene Design] by Boeke lab
 
*[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.
 
**Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.
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*[http://www.dna20.com/commerce/customer/emailsupp.jsp GeneDesigner] by DNA2.0
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**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.
  
 
*[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 17:44, 20 June 2006

<wikionly> Go to http://syntheticbiology.org/ </wikionly>

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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Home        About        Conferences        Labs        Courses        Resources        FAQ       

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
  • 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.
  • 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.

This site is hosted on OpenWetWare and can be edited by all members of the Synthetic Biology community.
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