* Predicted consensus values by the Splice Site Prediction Program: Neural Networks [23].
We next sought to correlate the presence of the predicted consensus sequence TGCATGCA AP2-exp binding motif in the upstream intergenic regions of the differentially expressed genes in our mutants.
The predicted consensus sequence TGCATGCA recognized by AP2-exp is found in the intergenic regions (−1500 bp) of 1485 predicted gene targets from plasmodb.org, while it is found 10,068 times in the whole P. falciparum genome (browsing the plasmoDB genome for the YRCATGYR pattern).
The error between the predicted consensus PFM and the real PFM is 0.04.
In order to discover detailed evolutionary information, we analyzed predicted consensus sequences as miRNA* sequences according to known miRNA* based on their precursor sequences.
We observed diminished luciferase activity in FXN promoter constructs that lack this intronic region (Figure 3A; constructs I and II), which contains a predicted consensus binding site for the EGR3 transcriptional regulator.
Some regions do contain a majority of predicted consensus "order".
Helix IV was conserved in all the predicted consensus secondary structures.
Unlike RSpredict that predicts consensus structures for multiple sequence alignments, alteRNA predicts secondary structures for single sequences.
When c1 is set to 0, the predicted consensus structures are less accurate than when c1 is set to −1.
