Visualization of a weights matrix
WeightsVis-Visualization of the positional weights matrix (PWM) calculated by TiCo for E. coli with the default parameters. The weights are provided with the TiCo-prediction (attached to the results-email for users of the web interface or written to the output directory of the stand-alone version). The tool WeightsVis is available from our download site. A short description of the usage is given in the README.
The plot shows the weights of the trinucleotides at the respective position in the extract range. The putative TIS are denoted at position zero. The upstream region is denote at positions with negative value, the downstream region is denoted with positive values, respectively. As it can be seen in the figure, the trinucleotide with the highest positive value is AGG at position -10. Also GAG, AGA and GGA have high positive values within that region. Obviously the high positive weights for these trinucleotides at position -12 ... -7 are associated with the Shine-Dalgarno sequence. Noteworthy are the triple-A-downstream box and a sequence of TAA occurences in the upstream region, which also seems to have a TIS-related information content.