Team:UNAM Genomics Mexico/Modeling/Cross Talk


Revision as of 21:38, 26 September 2012 by Abieltega (Talk | contribs)


=Cross Talk=

<img src="Unamgenomicsnanotubes.jpg" alt="some_text" height="200"/>


<img src="Unamgenomicsnanotubes1.jpg" alt="some_text" height="200"/>

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:




AraC belonging to E. coli

Bacillus subtilis promoters


AraR belonging to B. subtilis

Pbad/Pxyl promoter


LasR belonging to P. aeruginosa

Bacillus subtilis promoters


XylR belonging to B. subtilits

Pbad promoter


XylR belonging to E. coli

Bacillus subtilis promoters


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