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Team:TU Delft/project/software
From 2010.igem.org
(Difference between revisions)
(New page: ==Problem statement== In our project, we are taking genes from various organisms and putting them as a biobrick plasmid into E. coli. This may cause various unexpected problems in the new...) |
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==Searching for interactions== | ==Searching for interactions== | ||
| + | To get an idea of which interactions may occur, interactions within the original organisms where mapped to their E. coli homologs. | ||
| + | In more detail: | ||
| + | * Every introduced protein (See the coding [[Team:TU_Delft/project/biobricks|biobricks]]) was blast searched against the [http://string-db.org/newstring_cgi/show_input_page.pl?input_page_type=single_sequence STRING protein database]: | ||
| + | |||
| + | {| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1" | ||
| + | |'''Biobrick''' | ||
| + | |'''STRING Database ID''' | ||
| + | |- | ||
| + | |BBa_K398000 | ||
| + | |420246.GTNG_3499 | ||
| + | |- | ||
| + | |BBa_K398001 | ||
| + | |101510.RHA1_ro02534 | ||
| + | |- | ||
| + | |BBa_K398000 | ||
| + | |420246.GTNG_3499 | ||
| + | |- | ||
| + | |BBa_K398000 | ||
| + | |420246.GTNG_3499 | ||
| + | |- | ||
| + | |BBa_K398000 | ||
| + | |420246.GTNG_3499 | ||
| + | |} | ||
| + | |||
| + | |||
| + | ==Software development== | ||
| - | |||
==Result== | ==Result== | ||
Revision as of 14:44, 20 August 2010
Contents |
Problem statement
In our project, we are taking genes from various organisms and putting them as a biobrick plasmid into E. coli. This may cause various unexpected problems in the newly designed biological system:
- The protein in the original organism may need some other functional partners (proteins or RNAs) in order to behave correctly (I.A.W. a part of the imported system is missing)
- The introduced protein can interact with local proteins that are not ment to interact.
Searching for interactions
To get an idea of which interactions may occur, interactions within the original organisms where mapped to their E. coli homologs. In more detail:
- Every introduced protein (See the coding biobricks) was blast searched against the STRING protein database:
| Biobrick | STRING Database ID |
| BBa_K398000 | 420246.GTNG_3499 |
| BBa_K398001 | 101510.RHA1_ro02534 |
| BBa_K398000 | 420246.GTNG_3499 |
| BBa_K398000 | 420246.GTNG_3499 |
| BBa_K398000 | 420246.GTNG_3499 |
