# Team:UNAM Genomics Mexico/Modeling/Cross Talk

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## Revision as of 22:21, 26 September 2012

# Cross Talk

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:

**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

**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:

**For the intrinsic TF XylR in Bacillus subtilis compared against the promoter Pbad:**

Matrices

matrix name ncol nrow pseudo Wmin Wmax Wrange

1 matrix-scan_2012-09-23 23 6 0 -66.200 28.700 94.900 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 2012-09-23.134705

Job done 2012-09-23.134705

Seconds 0.13

user 0.13

system 0.03

cuser 0.1

csystem 0.02

Matrix logo:

**For XylR in Escherichia coli 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 -101.800 44.500 146.300 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 2012-09-23.135509

Job done 2012-09-23.135515

Seconds 0.4

user 0.4

system 0.01

cuser 0.1

csystem 0.02