TarPmiR

TarPmiR is a software tool developed for predicting microRNA (miRNA) target sites based on the analysis of CLASH (crosslinking ligation and sequencing of hybrids) data. The tool combines seven new features of miRNA target sites with existing ones used by other prediction algorithms to improve accuracy. TarPmiR was tested on two human and one mouse non-CLASH datasets and showed superior performance compared to three existing approaches in terms of recall and precision. The software is freely available and can be accessed online.

Topic

Functional, regulatory and non-coding RNA;RNA;Sequence analysis

Detail

  • Operation: miRNA expression analysis

  • Software interface: Command-line user interface

  • Language: Python

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: The National Science Foundation, the National Institute of Health.

  • Input: -

  • Output: -

  • Contact: jding@cs.ucf.edu;haihu@cs.ucf.edu;xiaoman@mail.ucf.edu

  • Collection: -

  • Maturity: -

Publications

  • TarPmiR: a new approach for microRNA target site prediction.
  • Ding J, et al. TarPmiR: a new approach for microRNA target site prediction. TarPmiR: a new approach for microRNA target site prediction. 2016; 32:2768-75. doi: 10.1093/bioinformatics/btw318
  • https://doi.org/10.1093/bioinformatics/btw318
  • PMID: 27207945
  • PMC: PMC5018371

Download and documentation

< Back to DB search