The main search page of "miRNA Prediction" allows the user to search two classes of miRNAs, those with supporting expression data (expressed type) and those predicted based on sequence conservation (conserved type).
In a second, more classical approach, we filtered the HMM-based motif cluster predictions based on sequence conservation of the predicted motifs themselves.
Based on sequence conservation and biochemical analysis, we predict that the Shroom-Rock interaction is highly conserved across animal evolution and represents a signaling module that is utilized in a variety of biological processes.
Based on sequence conservation, most zebrafish orthologues of human PTP genes were readily assigned.
Often gene functions of chicken genes were annotated based on sequence conservation without further functional evidence.
We identified 64 sRNAs in Shigella, which were experimentally validated in other bacteria based on sequence conservation.
Based on sequence conservation across species [14], this SNP is predicted to be relatively undamaging to protein function.
Based on sequence conservation, we identified 63 other sRNAs in Shigella which were experimentally validated (sRNAs were documented by Northern blot analysis, as shown in Table S1).
Based on sequence conservation, the strains that encode the rlrA islet can be grouped into three major clades that also correlate with the MLST clonal complexes [6].
Interestingly, it was predicted to be functional in a recent in silico study based on sequence conservation and density of potential transcription factor binding sites [29].
We also test a simpler method based on sequence conservation, which we name "Weighted sum" (WS), where we simply sum a weighted average of the motif score in the mouse and rat genome in addition to human.
