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pumpkin small RNAs

The pumpkin small RNA database contains all pumpkin small RNAs downloaded from Dr. Blake Meyer's small RNA site at University of Delaware. The small RNA datasets were combined by removing redundancies (same sequences, same lengths, and same directions). Currently the database contains ~9.4 million pumpkin small RNAs which represent more than 4.1 million unique small RNAs. Unique small RNAs derived from rRNA, tRNA, and repeats were identified and not included in the downstream analysis of miRNA identification. Small RNAs with counts less than ten in all individual samples were also not included in miRNA identification. The remaining small RNAs were then compared to miRBase to identify conserved miRNA candidates (up to two mismatches). Meantime, the small RNAs were aligned to the cucumber genome sequences and the flanking sequences (200bp to each side) of small RNAs with no more than 20 unique genome hits were extracted and then folded with the RNAfold program. The structures were then checked with miRcheck to identify potential miRNA candidates. The miRNA targets (cucumber, melon and watermelon unigenes) were identified using the target prediction tool developed and implemented in the database.