Tools

Our tools:

pirnaPre
    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.

Name Convert
    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.

Reverse Complement
    nucleotide sequence reverse complement tool.

Bowtie Online
    online bowtie tool.

Hypergeo Test
    hypergeometric test calculator.

CDS Format
    CDS sequence formatting tool.

Others related piRNA tools:

pirScan
    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.

2L-piRNA
    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.

piRPred
    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.