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Reverse target prediction tool

This page 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. Default settings are indicated below in the scoring system table. However, customized criteria can be entered by the user.

Also 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.

Please enter the genomic sequence into the box below. Fasta format should be used; the ">" symbol followed by the sequence name should precede the genomic sequence.

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Enter a genomic sequence to search for targets (in fasta format; only A, C, G, T allowed):





Or, upload your genomic sequence file to search for targets(Max 50 MB):

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Please select the small RNA library from the following lists for comparison to the DNA sequence that you have entered above.

Select Species:    Select Species Aristolochia fimbriata Amborella trichopoda Capsicum annum Chara corallina Cucurbita maxima Carica papaya Chlamydomonas reinhardtii Cycas rumphii Citrus sinensis Gossypium arboreum Ginkgo biloba Hordeum vulgare Lactuca sativa Musa acuminata Miscanthus giganteus Mimulus guttatus Marsilea quadrifolia Nuphar advena Nicotiana Tabacum Picea abies Persea americana Petunia hybrida Populus trichocarpa Panicum virgatum Sorghum bicolor Setaria italica Silene latifolia Solanum lycopersicum Solanum tuberosum Triticum aestivum Volvox carteri Vitis vinifera Zea mays Zostera marina Cleome Violacea Moringa Oleifera Tropaeolum Majus

Small RNA length: 18-22 bp    >22 bp

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Scoring system:	Default    Custom settings
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):	No    Yes
Filter:	10/11 nt positions - perfect match required 2 to 9 nt positions - no more than one mismatch allowed (forces most mismatches into 12 to 21 nt positions)

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