Upload miRNA/ta-siRNA sequence(s) in FASTA format:

The users upload miRNA and/or (transacting)ta-siRNA sequences of interest for searching target sequences. Before analysis, our pipeline will check and process the uploaded sequences based on below requirements:

• The sequences should be in FASTA format. A single sequence can also be directly submitted (without FASTA header).
  
• Users should submit 1-5000 sequences for analysis.
• Valid sequences should be between 16-28 nt in length.
• Only 'ATCGUN' are valid sequence letters, otherwise the sequence will be ignored.
• The letters ! % & " ' $ ` \ ^ * are not allowed in sequence ID, which will be automatically converted into "_" prior to analysis.
• If input FASTA format, please avoid too long sequences ID. For example, a ID longer than 50 letters may make the web display a mess.

Upload target candidate sequences in FASTA format:

The users upload potential target sequences of their interest. A typical target sequence may be a cDNA, EST, Unigene, mRNA or genomic segment, etc. The miRU2 server will search possible complemenrary regions between these submitted target sequences and miRNA/ta-simiRNA sequences. Before analysis, our pipeline will check and process the uploaded sequences based on below requirements:

• The sequences should be in FASTA format. A single sequence can also be directly submitted (without FASTA header).
• Users should submit 1 - 50,000 sequences for analysis.
• Valid sequences should be between 40 - 20,000 nt in length.
• Only 'ATCGUN' are valid sequence letters, other characters will be deleted or changed to 'N'.
• The letters ! % & " ' $ ` \ ^ * are not allowed in sequence ID, which will be automatically converted into "_" prior to analysis.
• If input FASTA format, please avoid too long sequence ID. For example, a ID longer than 50 letters may make the web display a mess.

Maximum expectation:

To score the complementary regions between miRNA/ta-siRNA and their target mRNA, we followed the method described by Yuanji Zhang(2005 PMID: 15980567). The maximum expectation is the threshold of the score. A complementary region will be discarded if its score is greater than the threshold.

Maximum circles:

Axtell et al 2006 (PMID: 17081978) proposed that multiply hits of a miRNA/ta-siRNA on a potential target sequence may facilitate the recognition between them. However, the stardard Smith-Waterman algorithm only gives the optimal hit on target sequence. We developed an iterative Smith-Waterman algorithm to overcome this limit by repeatedly calling Smith-Waterman program. The Maximum circles will limit the maximum times of calling. Increasing Maximum circles will increase the running time and get more possible complementary regions on a specific target sequences under maximum expectation.

Range of cleavage site in complimentary fragment (nt):

In addition to cleavage at post-transcriptional level, miRNA reportedly inhibits translation of target genes. It often happens when central mismatches occurs in complemetary fragment between miRNAs and target seuqneces because the central region is essential for recognition of cleavage (Brodersen et al 2008).
The users may set a expected range for the central mismatched region, i.e. range of cleavage site. The server will consider that a miRNA inhibit the tranlation of target sequences when mismatchs occur in this region.

Query tools bar on the top of list view page:

Query tools bar facilities users to filter/include complementary regions between miRNA/ta-siRNAs and target sequences based on keywords in target sequences' description/ID, miRNA ID and score threshold.