You can cite the paper:

Yuanji Zhang. (2005). miRU: an automated plant miRNA target prediction server. Nucleic Acids Res., (accepted)

 

Prediction Algorithm

The program implements with modifications for plant miRNA target prediction. It reports all potential sequences complementary to the query with mismatches no more than specified for each mismatch type. In addition, each mismatch is converted to a weighted score according to the algorithm (1) (a G:U scores 0.5, an indel 2.0 and any other mispair 1.0). Furthermore, any mismatch other than G:U wobble in the position 2 – 7 of the 5’ end of miRNA is penalized 0.5 extra points to reflect the importance of complementarity to the miRNA 5’ end for target site function (2-4). With default settings, the minimal score among all 20mers cannot exceed 3.0. This program can also be used for siRNA specificity detection.

 

Output Format

There are three parts in output page.

Part 1. Summary of query input information. It includes query miRNA, mismatches allowed, and target mRNA dataset. The following is an exampe query using ath_MIR162 to predict targets in Arabidopsis mRNA.

 

SUMMARY OF QUERY
Input miRNA: UCGAUAAACCUCUGCAUCCAG (21 nt)
Score allowed = 3
G:U pairs allowed = 6
Indels allowed = 1
Other mismatches allowed = 3
Target dataset = TIGR ATH1 (Arabidopsis mRNA) release 5
Homolog miRNA: UCGAUAAACCUCUGCAUCCAG (21 nt)
Dataset to be compared = TIGR Rice Genome mRNA (OSA1 release 3, 12/28/2004)

 

Part 2. A list of predicted complementary targets displayed in a table. However, the first row of the table is the query shown in 3' - 5'. For targets, the target gene ID, target site (start - end), best 20-mer score and number of mismatches are also shown in the table.The target sequence in 5' - 3' is shown with color code for mismatches (G:U, indel, and other mismatches). The conservation of target complementarity in the second dataset is indicated. Mouse-over the target ID will show the annotation and click the ID will go to the target gene sequence in the third part.

 
IDTarget Site AlignmentSiteScoreMismatchConserved
Query (3' - 5') GACCUACGUCUCCAAAUAGCU
At1g01040.1 cuggaugcagaggu uuaucga
              a 		3422 - 34432.51 y
At1g48430.1 cugggcgcagagguuuagcgg 565 - 58534
At2g23180.1 gaagaugcagagguuuauugg 730 - 75035

 

Part 3. The predicted target gene sequences. The sequence is shown in FASTA format, with target site highlighted in blue (see below). 

>At2g23180.1 68415.m02769 cytochrome P450, putative 
aagtattccaaaagaagaagaagaaatactttctcaattttctctaATGGCTCTGATAACCTTACTTGAAGTCTC
AATTTCTTTACTCTTTTTCTCCTTCCTTTACGGATATTTCTTGATTAGCAAGAAACCTCACCGTTCGTTTCTCAC
CAACTGGCCATTTCTCGGTATGCTTCCGGGTTTACTCGTGGAGATCCCTCGTGTTTACGACTTTGTAACCGAGCT
TCTCGAGGCCTCAAACTTAACTTATCCTTTCAAAGGTCCGTGTTTTGGGGGCCTTGACATGTTGATCACCGTTGA
TCCGGCTAATATCCATCACATCATGAGCTCAAACTTCGCGAATTACCCGAAAGGAACCGAGTTCAAGAAGATATT
CGATGTTTTGGGAGATGGGATTTTCAACGCGGATTCGGAGTTATGGAAAGATCTGAGGAAATCAGCTCAAAGCAT
GATGACTCATCAAGATTTTCAAAGGTTTACACTAAGAACAATCATGAGTAAGCTAGAGAAAGGGCTTGTCCCACT
TCTTGATTACGTTGCTGAAAAGAAACAAGTCGTTGACTTACAAGATGTGTTCCAAAGATTTACGTTCGACACTTC
GTTTGTTTTAGCGACCGGGGTTGACCCGGGTTGTCTCTCGACTGAAATGCCGCAAATCGAGTTTGCTAGAGCTTT
AGACGAAGCAGAGGAAGCAATTTTCTTCAGGCATGTGAAGCCAGAGATTGTTTGGAAGATGCAGAGGTTTATTGG
GTTTGGAGATGAGTTGAAAATGAAGAAAGCTCACTCGACATTCGACCGAGTTTGCTCTAAATGCATAGCTTCTAA
GAGAGATGAAATAACCAATGGGGTTATAAACATTGACTCTTCTTCTAAAGATTTGTTGATGTGCTACATGAATGT
GGATACAATTTGTCATACAACCAAGTACAAGTTGTTGAATCCAAGTGATGACAAATTCCTTAGAGACATGATCTT
AAGCTTCATGTTAGCTGGTAGAGACACCACAAGCTCTGCTCTCACTTGGTTCTTTTGGCTTCTCTCTAAGAACCC
AAAAGCCATAACCAAGATTCGTCAAGAAATCAACACACAACTATCTCCAAGAACCAATGATTTTGATTCATTCAA
TGCTCAAGAGTTAAACAAGTTGGTGTATGTACATGGAGCATTGTGTGAAGCCCTTAGGCTATATCCACCGGTTCC
ATTTCAGCACAAGTCTCCTACAAAATCCGACGTTCTTCCAAGTGGACACAGAGTCGATGCGAGTTCGAAGATTGT
GTTCTGTCTTTACTCATTAGGGAGAATGAAATCAGTTTGGGGAGAAGATGCATCGGAATTTAAACCGGAGAGATG
GATTTCAGAGAGTGGAAGGTTGATTCACGTGCCTTCTTTTAAGTTCTTATCGTTTAATGCCGGTCCAAGGACTTG
TTTGGGGAAAGAAGTGGCTATGACACAGATGAAGACAGTGGCTGTGAAAATTATACAAAACTATGAGATAAAGGT
CGTTGAAGGACACAAGATCGAGCCAGTTCCTTCTATTATTCTTCACATGAAGCATGGTCTTAAAGTTACAGTCAC
TAAGAGATCTAATTTGCTCTGAatattatgcattactattgtactacatttagtatgaaaataattattagaatt
ttacaaaatacttgaataagaggggtaatgtttacaat  









  

    
References

      
1. Jones-Rhoades, M.W. and Bartel, D.P. (2004) Computational identification 
        of plant microRNAs and their targets, including a stress-induced miRNA. 
        Mol. Cell, 14, 787-799. 

      
2. Mallory, A.C., Reinhart, B.J., Jones-Rhoades, M.W., Tang, G., Zamore, 
        P.D., Barton, M.K. and Bartel, D.P. (2004) MicroRNA control of PHABULOSA 
        in leaf development: importance of pairing to the microRNA 5' region. 
        EMBO J., 23, 3356-3364.

      
 3. Brennecke, J., Stark, A., Russell, R.B. and Cohen, S.M. (2005) Principles 
        of microRNA–target recognition. PLoS Biol., 3, e85.

      
 4. Lim, L.P., Lau, N.C., Garrett-Engele, P., Grimson, A., Schelter, 
        J.M., Castle, J., Bartel, D.P., Linsley, P.S. and Johnson, J.M. (2005) 
        Microarray analysis shows that some microRNAs downregulate large numbers 
        of target mRNAs. Nature, 433, 769-773.