| Overview |
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| Software |
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BlockSampler can be downloaded here.
Information on installation and parameters, can be found in the help file.
We also provide an example data set.
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BlockAligner can be downloaded here.
Information on installation and parameters, can be found in the help file.
An example data set can be found here.
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| Performance table |
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Supplementary information Table 1: this table contains the recovery rate, sensitivity and sensitivity of all four motifs (Fur, MetJ, LexA and PhoP) for all
three methologies (our methodology, MotifSampler, PhyloCon). It contains the numbers on which the plots of figure 3 are based.
The table can be found here or downloaded as pdf here.
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| Biological testcases |
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PmrA testcase
The first biological testcaste consisted of a list of 47 differentially expressed genes between a constitutive and a null pmrA mutant of S. typhimurium.
Applying our methodology resulted in two motif models. The first corresponded to the consensus of the biologically validated PmrA motif (consensus CTTAA-N5-CTTAA).
The instances of intergenic regions of the genes that contributed to the motif model, as well as the instances in intergenic regions of genes retrieved by screening with the deteteced motif model, can be found here.
In addition to the well known PmrA motif, we predicted yet an uncharacterized motif (consensus (T/A)AAGGAAnA). The detected instances can be found here.
FNR testcase
We applied our methodology to 83 genes that were differentially expressed in response to oxygen. This resulted in the detection of a motif model corresponding to the well known FNR motif.
Results can be found here.
Screening output of both results can also be downloaded as a pdf-file
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