PLEK

PLEK is a computational tool designed to identify long non-coding RNAs (lncRNAs) from de novo sequencing data, without prior gene annotations or genomic sequences. It uses an improved k-mer scheme and a support vector machine algorithm to distinguish lncRNAs from messenger RNAs (mRNAs) with high accuracy, achieving up to 95.6% accuracy on well-annotated human RefSeq mRNAs and GENCODE lncRNAs in 10-fold cross-validation tests. PLEK is also faster than other alignment-based or alignment-free tools and suitable for large-scale transcriptome data.

Topic

RNA-seq;Sequencing;Sequence assembly;Functional, regulatory and non-coding RNA

Detail

  • Operation: Nucleic acid feature detection;Filtering;RNA-Seq analysis

  • Software interface: Command-line user interface

  • Language: Python;C

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.2

  • Credit: Natural Science Foundation of China, the Research Fund for the Doctoral Program of Higher Education of China.

  • Input: -

  • Output: -

  • Contact: jyzhang@mail.xidian.edu.cn

  • Collection: -

  • Maturity: -

Publications

  • PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme.
  • Li A, et al. PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. 2014; 15:311. doi: 10.1186/1471-2105-15-311
  • https://doi.org/10.1186/1471-2105-15-311
  • PMID: 25239089
  • PMC: PMC4177586

Download and documentation

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