Synthetic Biology:Tools

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(DNA Tools)
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*[http://paris.chem.yale.edu/extinct.html Biopolymer calculator] by Schepartz lab
*[http://paris.chem.yale.edu/extinct.html 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
**Calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein
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*[http://synbio.mit.edu/tools/clipboard.cgi Clipboard] by [[Austin Che]]
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**Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence
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*[http://synbio.mit.edu/tools/converter.cgi File format converter] by [[Austin Che]]
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**Web tool for converting between sequence file formats.
*[http://slam.bs.jhmi.edu/gd/ Gene Design] by Boeke lab
*[http://slam.bs.jhmi.edu/gd/ Gene Design] by Boeke lab
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===Protein Tools===
===Protein Tools===
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*[http://ncbi.nih.gov/Structure/CN3D/cn3d.shtml Cn3D] by NCBI
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**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.
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*[http://www.expasy.org/spdbv/ DeepView] by GlaxoSmithKline & Swiss Institute of Bioinformatics
*[http://www.expasy.org/spdbv/ DeepView] by GlaxoSmithKline & Swiss Institute of Bioinformatics
**Awesome program for viewing and studying protein structure.
**Awesome program for viewing and studying protein structure.
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*[http://us.expasy.org/ ExPASy Proteomics server] by the Swiss Institute of Bioinformatics  
*[http://us.expasy.org/ ExPASy Proteomics server] by the Swiss Institute of Bioinformatics  
**Collection of links to many pages to calculate parameters of your favorite proteins
**Collection of links to many pages to calculate parameters of your favorite proteins
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*[http://salilab.org/modeller/ Modeller] by Sali Lab
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**For homology or comparative modeling of protein three-dimensional structures.
*[http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php Zinc Finger Tools] by Barbas Lab
*[http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php Zinc Finger Tools] by Barbas Lab

Revision as of 10:56, 3 October 2005

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Online Tools

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.
  • 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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