Orchid Small RNA Target Prediction
This page can be used to predict targets of small RNA sequences such as microRNAs.
The target prediction program identifies potential targets of microRNAs
or other small RNAs in the genome or set of sequences that you chose or submit.
This algorithm generates a score based on mismatches and bulges, and the settings
can be used as defined by Jones-Rhoades and Bartel, or customized to fit your
needs. In the default settings, a mismatch is given a score of 1, a wobble (G:U
mismatch ) is given a score of 0.5 and a bulge is given a score of 2. As
an example, this means that a score of 2 can correspond to genomic targets
that match the small RNA with 4 wobbles, or 2 mismatches, or 1 bulge, or 2
wobbles & 1 mismatch. The results may be incomplete due to the use of specific "seeds"
in the matching algorithm, but it is hard to predict which matches may be be missed.
Please enter the small RNA sequence(s) of up to 30 nucleotides into the box below;
lists of sequences can be separated by carriage returns (no commas or semicolons).
The algorithm is based on that described by Matthew Jones-Rhoades and David Bartel,
of MIT; they describe this method in Molecular Cell, Volume 14, 787-799. The default
settings are described below.
Sample output (for Arabidopsis)