a SVM classifier based on a combination of Miwi CLIP-Seq derived features and position derived features to predict potential targets of piRNAs on mRNAs.
convert a list of NCBI or RNAdb piRNA names and accession numbers to piRBase names.
Seq To Name
retrieve piRBase names by a list of piRNA sequences.
nucleotide sequence reverse complement tool.
online bowtie tool.
hypergeometric test calculator.
CDS sequence formatting tool.
a web-based tool published in 2018 for identifying C. elegans piRNA-targeting sites within a given mRNA or spliced DNA sequence.
Ref:Wu, W.S., Huang, W.C., Brown, J.S., Zhang, D., Song, X., Chen, H., Tu, S., Weng, Z. and Lee, H.C. (2018) pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans. Nucleic acids research, 46, W43-W48.
a two-layer ensemble classifier for identifying piRNAs and their function.
Ref:Liu, B., Yang, F. and Chou, K.C. (2017) 2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function. Mol Ther Nucleic Acids, 7, 267-277.
a multiple kernel-based SVM algorithm for piRNA identification
Ref:Brayet, J., Zehraoui, F., Jeanson-Leh, L., Israeli, D. and Tahi, F. (2014) Towards a piRNA prediction using multiple kernel fusion and support vector machine. Bioinformatics, 30, i364-370.