Team:ETH Zurich/Modeling/Genome Static Analysis

From 2008.igem.org

(Difference between revisions)
(→Restriction Enzyme Analysis)
(→Restriction Enzyme Analysis)
Line 12: Line 12:
<!-- PUT THE PAGE CONTENT AFTER THIS LINE. THANKS :) -->
<!-- PUT THE PAGE CONTENT AFTER THIS LINE. THANKS :) -->
==Restriction Enzyme Analysis==
==Restriction Enzyme Analysis==
 +
 +
This section presents the computational investigation we performed in order to understand which restriction enzymes are optimal when used in our minimal genome approach, in order to find out which restriction enzymes cut the genome in fragments that most probably will lead to find the minimal genome. Important is to note that this is a "statical" analysis, meaning that we do not include any prevision regarding to the effects on cell physiology or cell system behaviour to our evaluation of the restriction enzymes. We focus here only on the information that can be obtained using  three informations:
 +
 +
* the genome sequence of our strain of interest (E.Coli K12 MG1655).
 +
* the annotation information of our strain of interest (E.Coli K12 MG1655).
 +
* recognition sites of each of the restriction enzymes we test.
 +
 +
We addressed questions regarding the cell system response after genome reduction using more advanced modelling techniques (a genome scale model) in the [[Genome Scale Analysis|Genome Scale Analysis section]].
 +
 +
 +
 +
 +
we made in order to select which restriction enzyme(s) should we use in our reduction strategies in order to optimize our goal, namely to reduce the genome as much as possible without losing
 +
[[Team:ETH_Zurich/Modeling/Genome_Static_Analysis/RestrictionTable|Table with restriction enzymes analysis]].
[[Team:ETH_Zurich/Modeling/Genome_Static_Analysis/RestrictionTable|Table with restriction enzymes analysis]].

Revision as of 15:24, 25 October 2008


Restriction Enzyme Analysis

This section presents the computational investigation we performed in order to understand which restriction enzymes are optimal when used in our minimal genome approach, in order to find out which restriction enzymes cut the genome in fragments that most probably will lead to find the minimal genome. Important is to note that this is a "statical" analysis, meaning that we do not include any prevision regarding to the effects on cell physiology or cell system behaviour to our evaluation of the restriction enzymes. We focus here only on the information that can be obtained using three informations:

  • the genome sequence of our strain of interest (E.Coli K12 MG1655).
  • the annotation information of our strain of interest (E.Coli K12 MG1655).
  • recognition sites of each of the restriction enzymes we test.

We addressed questions regarding the cell system response after genome reduction using more advanced modelling techniques (a genome scale model) in the Genome Scale Analysis section. 



we made in order to select which restriction enzyme(s) should we use in our reduction strategies in order to optimize our goal, namely to reduce the genome as much as possible without losing


Table with restriction enzymes analysis.
Retrieved from "http://2008.igem.org/Team:ETH_Zurich/Modeling/Genome_Static_Analysis"