Rice 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.

Enter small RNA sequence(s)
Enter small RNAs to search for targets:
Note: sequences must be in FASTA format with the ">name" proceeding each sequence; no blank lines separating sequences are permitted. Sequences must be 17-30 nucleotides; only A, U, C, G, T are allowed.

Or, upload your small RNA sequence file to search for targets:

Select scoring system
Scoring system: Default   
Enter score: < =     Bulge    Mismatch   Wobble
(enter score values in the format 1.0, 1.5, 2.0 )
Filter: 10/11 nt positions - perfect match required
2 to 9 nt positions - no more than one mismatch allowed (forces most mismatches into 12 to 21 nt positions)
Ignore penalty scores for a mismatch at the first (5') position of the small RNA.

Find targets in dataset:   
Find targets for a particular sequence(s) in your dataset file.

Upload your chromosome file to search for targets (fasta format, 50 Mb maximum):

Send results to
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Sample output (for Arabidopsis)