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

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

• 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, pssRNATarget added two new search functions. Now, the pssRNATarget 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 pssRNATarget 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 pssRNATarget 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 pssRNATarget databases.
  

» Visit pssRNATarget

In plants, short RNAs including ~21-nt microRNA (miRNA) and 21-nt trans-acting siRNA (ta-siRNA) compose a "miRNA -> ta-siRNA -> target gene" cascade pathway that regulates gene expression at the post-transcriptional level. In this cascade, biogenesis of ta-siRNA clusters requires 21-nt intervals (i.e. phasing) and miRNA (phase-initiator) cleavage sites on its TAS transcript. Here we report a novel web server, pssRNAMiner, which is developed to identify both the clusters of phased small RNAs as well as the potential phase-initiator.

• To detect phased small RNA clusters, the pssRNAMiner maps input small RNAs against user-specified transcript/genomic sequences, and then identifies phased small RNA clusters by evaluating P values of hypergeometric distribution.
  
• To identify potential phase-initiators, pssRNAMiner aligns input phase-initiators with transcripts of TAS candidates using the Smith-Waterman algorithm. Potential cleavage sites on TAS candidates are further identified from complementary regions by weighting the alignment expectation and its distance to detected phased small RNA clusters.

» Visit pssRNAMiner

Personal-bLAst Navigator (PLAN) is a web application for organizing, managing and mining sequence alignment results based on BLAST search. Current features of PLAN include

• Project based data organization;
• Management of interesting queries and targets through favorites;
• Statistical overview by query, target, gene line and plate (if applicable);
• Alignment visualization;
• Filtering by match score and e-value;
• Search by accession, name and description.

PLAN also can be easily integrated into other web applications for the visualization of BLAST alignment.

» Visit PLAN Server

phpSSRMiner effectively streamlines the process of SSR (Simple Sequence Repeat) identification, primer design, and in-silicon primer verification in a single web interface. Sequences are managed in different libraries. SSRs and primers are searchable in different manners.

» Visit phpSSRMiner Server