Team:TU Delft/project/software

From 2010.igem.org

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|'''STRING Database ID'''
|'''STRING Database ID'''
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|-
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|BBa_K398000
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|[http://partsregistry.org/Part:BBa_K398000 BBa_K398000]
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|420246.GTNG_3499
+
|[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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|BBa_K398001
+
|[http://partsregistry.org/Part:BBa_K398001 BBa_K398001]
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|101510.RHA1_ro02534
+
|[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]
|-
|-
-
|BBa_K398000
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|[http://partsregistry.org/Part:BBa_K398002 BBa_K398002]
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|420246.GTNG_3499
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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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|BBa_K398000
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|[http://partsregistry.org/Part:BBa_K398003 BBa_K398003]
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|420246.GTNG_3499
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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]
|-
|-
-
|BBa_K398000
+
|[http://partsregistry.org/Part:BBa_K398004 BBa_K398004]
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|420246.GTNG_3499
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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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|[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]
 +
|-
 +
|[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]
 +
|-
 +
|[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]
 +
|-
 +
|[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]
 +
|-
 +
|[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]
 +
|[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]
 +
|-
 +
|[http://partsregistry.org/Part:BBa_K398401 BBa_K398401]
 +
|[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]
|}
|}
 +

Revision as of 14:45, 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 [http://string-db.org/newstring_cgi/show_input_page.pl?input_page_type=single_sequence STRING protein database]:
Biobrick STRING Database ID
[http://partsregistry.org/Part:BBa_K398000 BBa_K398000] [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]
[http://partsregistry.org/Part:BBa_K398001 BBa_K398001] [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]
[http://partsregistry.org/Part:BBa_K398002 BBa_K398002] [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]
[http://partsregistry.org/Part:BBa_K398003 BBa_K398003] [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]
[http://partsregistry.org/Part:BBa_K398004 BBa_K398004] [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]
[http://partsregistry.org/Part:BBa_K398005 BBa_K398005] [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]
[http://partsregistry.org/Part:BBa_K398006 BBa_K398006] [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]
[http://partsregistry.org/Part:BBa_K398100 BBa_K398100] [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]
[http://partsregistry.org/Part:BBa_K398200 BBa_K398200] [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]
[http://partsregistry.org/Part:BBa_K398201 BBa_K398201] [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]
[http://partsregistry.org/Part:BBa_K398300 BBa_K398300] [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]
[http://partsregistry.org/Part:BBa_K398400 BBa_K398400] [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]
[http://partsregistry.org/Part:BBa_K398401 BBa_K398401] [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]


Software development

Result

Retrieved from "http://2010.igem.org/Team:TU_Delft/project/software"