Reverse Target Prediction

This tool is based on more typical target prediction programs used to predict targets of small RNA sequences such as microRNAs – BUT, since no genome may be available or since you may have a genomic sequence that you would like to assess for targets of small RNAs, we have developed a “reverse target prediction” algorithm. In this case, the user enters a genomic sequence, and then picks a set of small RNAs to compare against that sequence. In some cases, it may be possible to use this page with the output of another of our small RNA analysis pages. Because this is a computationally intensive search (due to the mismatches permitted for miRNA targets), we limit the size of the input sequence. The result will be a set of small RNAs that match the input sequence with the characteristics of a miRNA.

Mismatches and wobbles (G:U mismatches) are given a score based on their position on the alignment between the input sequence and the putative small RNA targeting it. Final scores are provided as sum of single scores over the entire alignment. Gapped alignments are not allowed.


Enter/upload a genomic sequence An input sequence can be either entered directly to the text area or uploaded as a file (max file size =50 MB). Fasta format should be used; the “>” symbol followed by the sequence name should precede the genomic sequence. Only A, C, G, T are allowed.








Select/enter/upload small RNA sequences You can select miRNA sequences from various organisms, or you can provide your own small RNA sequences by either entering them directly to the text area or uploading them as a file (max file size =50 MB). Please have one sequence on each line, or fasta format (the “>” symbol followed by the sequence name preceding the sequence) is also accepted.
Note: Only A, C, G, T are allowed. If the sequence provided contains a 'U', it will be converted to a 'T' and processed.

  


Select small RNA length To minimize the computational time, we require that the user select smaller molecules (18-22 nt) or larger molecules (>22 nt). Since miRNAs are usually 20-22 nt, we recommend using the smaller class.


Select settings for the scoring system Default settings are indicated in the table below, but you can enter customized criteria instead.

Use:
Enter maximum number of mismatches allowed (inclusive of all non-canonical Watson & Crick pairings):
Enter value for wobble pairing in: 2 to 7 nt positions =
10 to 11 nt positions =
Enter value for wobble pairing in all other positions:
Enter value for other non-canonical Watson & Crick pairing in: 2 to 7 nt positions =
10 to 11 nt positions =
Enter value for other non-canonical Watson & Crick pairing in all other positions:
Do you want the best score in 20 consecutive nucleotides (when length > 20):
Filter:
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Sample output