Team:TU Delft/project/software

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__NOTOC__
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#REDIRECT [[Team:TU Delft/Modeling/interaction-mapping]]
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==Problems with introducing new genes==
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In our project, we are taking genes from various organisms and putting them as a biobrick plasmid into E. coli.
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This may cause various unexpected problems in the newly designed biological system:
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* 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)
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* The introduced protein can interact with local proteins that are not ment to interact.
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==Searching for interactions==
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To get an idea of which interactions may occur, interactions within the original organisms where mapped to their E. coli homologs:
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[[Image:IGEMTUDelft_Interactiongraph.PNG]]
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In more detail:
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* The sequence of every introduced protein (See the coding [[Team:TU_Delft/project/biobricks|biobricks]]) was blasted against the [http://string-db.org/newstring_cgi/show_input_page.pl?input_page_type=single_sequence STRING protein database]. This resulted in a number of proteins that are either the correct proteins, or homologs of the introduced proteins.
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{| style="color:black; background-color:white;" cellpadding="5" cellspacing="0" border="1"
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|'''Biobrick'''
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|'''STRING Database ID'''
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|-
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|[http://partsregistry.org/Part:BBa_K398000 BBa_K398000]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=420246.GTNG_3499&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 420246.GTNG_3499]
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|-
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|[http://partsregistry.org/Part:BBa_K398001 BBa_K398001]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=101510.RHA1_ro02534&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 101510.RHA1_ro02534]
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|-
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|[http://partsregistry.org/Part:BBa_K398002 BBa_K398002]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=246196.MSMEG_1840&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 246196.MSMEG_1840]
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|-
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|[http://partsregistry.org/Part:BBa_K398003 BBa_K398003]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=350058.Mvan_1744&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 350058.Mvan_1744]
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|-
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|[http://partsregistry.org/Part:BBa_K398004 BBa_K398004]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=101510.RHA1_ro02537&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 101510.RHA1_ro02537]
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|-
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|[http://partsregistry.org/Part:BBa_K398005 BBa_K398005]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=235909.GK0984&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 235909.GK0984]
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|-
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|[http://partsregistry.org/Part:BBa_K398006 BBa_K398006]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=235909.GK2772&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 235909.GK2772]
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|-
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|[http://partsregistry.org/Part:BBa_K398100 BBa_K398100]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=7227.CG4651-PA&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 7227.CG4651-PA]
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|[http://partsregistry.org/Part:BBa_K398200 BBa_K398200]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=62977.ACIAD0697&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 62977.ACIAD0697]
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|[http://partsregistry.org/Part:BBa_K398201 BBa_K398201]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=160488.PP_0504&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 160488.PP_0504]
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|-
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|[http://partsregistry.org/Part:BBa_K398300 BBa_K398300]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=399739.Pmen_0429&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 399739.Pmen_0429]
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|[http://partsregistry.org/Part:BBa_K398400 BBa_K398400]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=70601.PH0527&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 70601.PH0527]
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|-
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|[http://partsregistry.org/Part:BBa_K398401 BBa_K398401]
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|[http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=70601.PH0532&all_channels_on=1&interactive=yes&network_flavor=evidence&targetmode=proteins 70601.PH0532]
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|}
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* For each protein, the interactions stored in STRING where gathered.
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* For each found interacting protein, E. coli homologs where gathered.
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* This results in a combination of interactions with their E. coli homologs. The likelyness of this being a true interaction depends on the STRING interaction score (Data from publication text mining, microarrays and other sources) and the BLAST score (The homolog mapping step).
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==Software development==
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An application was developed that can run these queries on a PostgreSQL server running the [http://string-db.org/newstring_cgi/show_download_page.pl STRING database]. This database can be downloaded for free for academic use. Unfortunately, the STRING API does not provide enough functionality to do the homolog mapping, so a PostgreSQL database with the STRING data is always needed.
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Source will be provided once the application is done.
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==Result==
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TODO..
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Latest revision as of 22:26, 12 September 2010

  1. REDIRECT Team:TU Delft/Modeling/interaction-mapping
Retrieved from "http://2010.igem.org/Team:TU_Delft/project/software"