User:Pakpoom Subsoontorn/Notebook/Genetically Encoded Memory/2008/10/14: Difference between revisions

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==Tools==
==Tools==
Informatics tools
* automated system of updating the list of information in public domain.
** The list of enzymes and the reference scientific literature (i.e. from pubmed)
** Roughly split-up information types:
** Standard information such as sequence, structure, ontology, etc from GenBank or PDB
Molecular Biology tools
* Standard cassettes on plasmids so that we can try wide varieties of recombination sites and recombination enzymes
* Standard cassettes on plasmids so that we can try wide varieties of recombination sites and recombination enzymes
* Tunable promoter and some reporter tags that report the levels of recombinase
* Tunable promoter and some reporter tags that report the levels of recombinase

Revision as of 02:03, 19 October 2008

Project name <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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Quantitative functional profiles of site-specific recombinase

  • Insert content here...

Quantitative functional information

Key feature of the database

  • Quantitative description
  • Capabilities to compare and contrast

The list of things we want to measure and compare:

  • Recombination efficiency
  • Recombination speed

Parameter we want to tune,

  • Enzyme concentration
  • Expression time
    • How long do we have to have enzyme around?

Database/method features

  • Expandable size of database without messing up with core structure
  • literature cross reference, updating
  • scalable experiment/measurement

Tools

Informatics tools

  • automated system of updating the list of information in public domain.
    • The list of enzymes and the reference scientific literature (i.e. from pubmed)
    • Roughly split-up information types:
    • Standard information such as sequence, structure, ontology, etc from GenBank or PDB


Molecular Biology tools

  • Standard cassettes on plasmids so that we can try wide varieties of recombination sites and recombination enzymes
  • Tunable promoter and some reporter tags that report the levels of recombinase
  • Method for timing the recombination process. At what time point the recombination of DNA is complete? This could time scale could be much shorter than the time until the reporter of the new DNA configuration become observable. Can we pause/terminate recombination at different time point?
  • Some mechanism to accommodate the fact that the substrate (sites on genomic DNA) has very low copies.


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