Team:UNAM Genomics Mexico/Modeling/Cross Talk

From 2012.igem.org

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=Cross Talk=
=Cross Talk=
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<table border="0"  height="300" cellspacing="15" bgcolor="transparent" id="tablecontentbg">
<table border="0"  height="300" cellspacing="15" bgcolor="transparent" id="tablecontentbg">
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<td id="leftcolumn2" align="center"><img src="http://2012.igem.org/wiki/images/d/d2/Unamgenomicsnanotubes.jpg" alt="some_text" height="200"/><br /><br /><p>Nanotubes</p></td>
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<td id="leftcolumn2" align="center">abi<br /><br /><p>Nanotubes</p></td>
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<td  id="contentcolumn2" align="center"><img src="http://2012.igem.org/wiki/images/9/96/Unamgenomicsnanotubes1.jpg" alt="some_text" height="200"/><br /><br /><p>The logic</p></td>
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<td  id="contentcolumn2" align="center">abi1<p>The logic</p></td>
<td id="rightcolumn2">Random info</td>
<td id="rightcolumn2">Random info</td>
</tr>
</tr>
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matrix name                  matches scored<br />
matrix name                  matches scored<br />
1 matrix-scan_2012-09-23 0 0<br />
1 matrix-scan_2012-09-23 0 0<br />
-
              TOTAL          0 0<br />
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TOTAL          0 0<br />
Host name miztli.nnb.unam.mx<br />
Host name miztli.nnb.unam.mx<br />
Job started 2012-09-23.134423<br />
Job started 2012-09-23.134423<br />
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The logo of the matrix used:<br />
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[[File:File:Unamgenomicsmodellogo1.jpg]]<br />
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'''For AraR compared against the promoter Pbad:'''<br />
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Matrices<br />
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matrix name                  ncol nrow pseudo Wmin Wmax Wrange<br />
 +
1 matrix-scan_2012-09-23 16 6 0 -47.000 16.000 63.000 a:0.291 c:0.207 g:0.204 t:0.297 <br />
 +
Number of sequences scanned 0<br />
 +
Sum of sequence lengths 0<br />
 +
N residues          0<br />
 +
Matches per matrix<br />
 +
matrix name                  matches scored<br />
 +
1 matrix-scan_2012-09-23 0 0<br />
 +
TOTAL          0 0<br />
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Host name miztli.nnb.unam.mx<br />
 +
Job started 2012-09-23.135941<br />
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Job done 2012-09-23.135941<br />
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Seconds 0.14<br />
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user 0.14<br />
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system 0.02<br />
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cuser 0.1<br />
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csystem 0.02<br />
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<br />
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<br />
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<br />
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[[File:Unamgenomicsmodellogo2.jpg]]<br />
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<br />
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<br />
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'''For LasR compared against the promoters in Bacillus subtilis strain 168''':<br />
 +
 +
Matrices<br />
 +
matrix name                  ncol nrow pseudo Wmin Wmax Wrange<br />
 +
1 matrix-scan_2012-09-23 16 6 0 -47.500 13.500 61.000 a:0.327 c:0.165 g:0.193 t:0.314<br />
 +
Number of sequences scanned 4176<br />
 +
Sum of sequence lengths 498968<br />
 +
N residues          14<br />
 +
Matches per matrix<br />
 +
matrix name                  matches scored<br />
 +
1 matrix-scan_2012-09-23 0 0<br />
 +
TOTAL          0 0<br />
 +
Host name miztli.nnb.unam.mx<br />
 +
Job started 2012-09-23.140435<br />
 +
Job done 2012-09-23.140437<br />
 +
Seconds 0.4<br />
 +
user 0.4<br />
 +
system 0.02<br />
 +
cuser 0.09<br />
 +
csystem 0.03<br />
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The logo of the matrix:<br />
-
The logo of the matrix used:
 
}}
}}

Revision as of 22:02, 26 September 2012


UNAM-Genomics_Mexico

=Cross Talk=

abi

Nanotubes

abi1

The logic

Random info




Due to the fact that our construction introduces exogenous transcription factors to the cell, we wanted to make sure that there would be no crosstalk, meaning that they wouldn’t recognize other promoters and create noise in the system. For this purpose, we downloaded weight matrixes for the sequences recognized by our transcription factors from PRODORIC database, and we downloaded the sequences for promoters (-200, +50 parting from the TSS) using retrieve sequence from RSA-tools. We chose Bacillus subtilis strain 168 because our strain is a derivative of this strain (I like the word strain…strain, strain, strain yay!). After that, we used quick matrix-scan in RSA-tools (Regulation Sequence Analysis-tools) to compare the sequences of the promoters to the weight matrixes to see if any of our transcription factors could bind in a troublesome place. We soon found out that this was not the case. Satisfied with our new-found self-confidence, we proceeded undauntedly to explore the more obscure parts of our project as our doubts wore away in the computational demonstration that they were, in fact, unworthy of being called truths. Here are the boring details of the deed: Details summary:

Tf

Sequence

Matches

AraC belonging to E. coli

Bacillus subtilis promoters

0

AraR belonging to B. subtilis

Pbad/Pxyl promoter

0

LasR belonging to P. aeruginosa

Bacillus subtilis promoters

0

XylR belonging to B. subtilits

Pbad promoter

0

XylR belonging to E. coli

Bacillus subtilis promoters

0


For AraC compared against the promoters in Bacillus subtilis strain 168:
Matrices
matrix name ncol nrow pseudo Wmin Wmax Wrange

1 matrix-scan_2012-09-23 33 6 0 -101.700 44.600 146.300 a:0.327 c:0.165 g:0.193 t:0.314
Number of sequences scanned 4176
Sum of sequence lengths 498968
N residues 14
Matches per matrix
matrix name matches scored
1 matrix-scan_2012-09-23 0 0
TOTAL 0 0
Host name miztli.nnb.unam.mx
Job started 2012-09-23.134423
Job done 2012-09-23.134424
Seconds 0.39
user 0.39
system 0.02
cuser 0.09
csystem 0.03


The logo of the matrix used:

File:File:Unamgenomicsmodellogo1.jpg


For AraR compared against the promoter Pbad:
Matrices
matrix name ncol nrow pseudo Wmin Wmax Wrange
1 matrix-scan_2012-09-23 16 6 0 -47.000 16.000 63.000 a:0.291 c:0.207 g:0.204 t:0.297
Number of sequences scanned 0
Sum of sequence lengths 0
N residues 0
Matches per matrix
matrix name matches scored
1 matrix-scan_2012-09-23 0 0
TOTAL 0 0
Host name miztli.nnb.unam.mx
Job started 2012-09-23.135941
Job done 2012-09-23.135941
Seconds 0.14
user 0.14
system 0.02
cuser 0.1
csystem 0.02



Unamgenomicsmodellogo2.jpg


For LasR compared against the promoters in Bacillus subtilis strain 168:

Matrices
matrix name ncol nrow pseudo Wmin Wmax Wrange
1 matrix-scan_2012-09-23 16 6 0 -47.500 13.500 61.000 a:0.327 c:0.165 g:0.193 t:0.314
Number of sequences scanned 4176
Sum of sequence lengths 498968
N residues 14
Matches per matrix
matrix name matches scored
1 matrix-scan_2012-09-23 0 0
TOTAL 0 0
Host name miztli.nnb.unam.mx
Job started 2012-09-23.140435
Job done 2012-09-23.140437
Seconds 0.4
user 0.4
system 0.02
cuser 0.09
csystem 0.03

The logo of the matrix: