psRNATarget: A Plant Small RNA Regulator Target Analysis Server

The psRNATarget server was developed to update the miRU: an automated plant miRNA target prediction server, Nucl Acids Res 33 (2005), W701-704.

The psRNATarget accepts miRNA/ta-siRNA mature sequences and target candidates as inputs. It reports all potential complementary regions between miRNA/ta-siRNA and target sequences using an improved iterative parallel Smith-Waterman algorithm and a weighted scoring schema allowing each mismatch being penalized according to the mismatch type and position in the query small RNA.

The psRNATarget provides significant updates and more importantly, a number of new functions. For example,

• Our new algorithm considers Brodersen et al.’s new discovery suggesting that plant miRNAs also inhibit translation of target gene when the central mismatches occur in miRNA/mRNA complementary region.


• We developed a iterative parallel Smith-Waterman based algorithm to search all possible complementary regions on each potential target transcript. This improvement overcomes the traditional Smith-Waterman algorithm’s limit on only finding the “optimal” hit on target sequence. The new algorithm considers the multiple complementary regions of a miRNA/ta-siRNA on one target sequence, which facilitate the recognition between the small RNA and the target transcript . This improvement is very helpful in searching potential miRNA phase-initiator of a TAS gene.


• In addition to search potential targets of user-submitted small RNA in published transcript libraries, psRNATarget added two new search functions. Now, the psRNATarget is able to (1) search whether the user-submitted sequences are potential targets of published miRNA/ta-siRNA sequences, and (2) search user-submitted small RNA against user-submitted target candidates. And, the psRNATarget server automatically synchronizes with miRBase to keep the published miRNA dataset up-to-date. The two new functions are highly desired by our miRU users worldwide.


• The previous miRU only analyzes one miRNA per run, while psRNATarget is able to search thousands of miRNA/siRNA against genome-scale (tens of thousands) target candidates per run thanks to our newly developed backend network-based parallel searching algorithms.


• Last but not the least; we have kept the Plant UniGene libraries and gene model transcript libraries up-to-dated in our psRNATarget databases.

The psRNATarget web server is freely available at http://bioinfo3.noble.org/psRNATarget/. To contact us, please write to: bioinfo@noble.org

Citation(s): Xinbin Dai and Patrick Xuechun Zhao. psRNATarget: A Plant Small RNA Regulator Target Analysis Server, manuscript under preparation.