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Citations per year

Number of citations per year for the bioinformatics software tool PLEK
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Protocols

PLEK specifications

Information


Unique identifier OMICS_05839
Name PLEK
Alternative name predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Junying Zhang

Publication for predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

PLEK citations

 (25)
library_books

Cross species inference of long non coding RNAs greatly expands the ruminant transcriptome

2018
PMCID: 5926538
PMID: 29690875
DOI: 10.1186/s12711-018-0391-0

[…] vides additional evidence for 650 existing Oar v3.1 lncRNA models (Additional file : Table S1). A small proportion of longlisted gene models were considered non-coding by at least one of CPC, CPAT or PLEK, nevertheless they showed some degree of sequence homology to either a known protein or protein domain: for sheep, 226 (including 13 existing Oar v3.1 models) [see Additional file : Table S4], an […]

library_books

Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre weaning calves in response to different diets

2018
Oncotarget
PMCID: 5940403
PMID: 29765519
DOI: 10.18632/oncotarget.24898

[…] r different, independent bioinformatic lncRNA prediction tools were applied in parallel: three alignment-free algorithms, CNCI [Coding-Non-Coding Index, [], https://github.com/www-bioinfo-org/CNCI)], PLEK [(Predictor of long non-coding RNAs and messenger RNAs based on k-mer scheme, [], https://sourceforge.net/projects/plek/files/)] and FEELnc [(FlExible Extraction of long NonCoding RNAs, https://g […]

library_books

Integrated DNA methylome and transcriptome analysis reveals the ethylene induced flowering pathway genes in pineapple

2017
Sci Rep
PMCID: 5719354
PMID: 29215068
DOI: 10.1038/s41598-017-17460-5

[…] fcompare, the reads were compared to the genome annotation, and then AS isoforms and APA isoforms were obtained. Then, the coding potentiality of the remaining reads was predicted using CPC, CPAT and PLEK. According the results, novel coding and non-coding transcripts were predicted. In addition, reads that mapped to miRNA and phasi-siRNA loci were also extracted.To predict lncRNA targets, we pred […]

library_books

Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment

2017
Sci Rep
PMCID: 5656573
PMID: 29070806
DOI: 10.1038/s41598-017-14451-4

[…] an 200 nt. The coding capacity of all of the novel transcripts was assessed with the coding potential assessment tool (CPAT) and the predictor of long non-coding RNAs and mRNAs based on k-mer scheme (PLEK). CPAT applies logistic regression algorithm to discriminate between coding and noncoding transcripts based on the following sequence features: open reading frame size, open reading frame coverag […]

call_split

Transcriptomic Analysis of Long Non Coding RNAs and Coding Genes Uncovers a Complex Regulatory Network That Is Involved in Maize Seed Development

2017
Genes
PMCID: 5664124
PMID: 29039813
DOI: 10.3390/genes8100274
call_split See protocol

[…] e strand, transcripts with FPKM scores <1, transcripts shorter than 200‚ÄČnt, and an exon number of less than 2. We used the Coding Potential Calculator (CPC) [], Coding-Non-Coding index (CNCI) [], and predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme (PLEK) [] to filter transcripts with coding potential. The remaining transcripts with known protein domains were […]

library_books

Transcriptome analysis of Callery pear (Pyrus calleryana) reveals a comprehensive signalling network in response to Alternaria alternata

2017
PLoS One
PMCID: 5608294
PMID: 28934298
DOI: 10.1371/journal.pone.0184988

[…] n improved k-mer scheme and a support vector machine algorithm []. Approximately 1730 novel transcripts were identified to be potential lncRNA transcripts by the intersection results of CPC, CNCI and PLEK software (). The lncRNAs were shorter than coding RNAs, with an average length of 564 bp. The lengths of 409 lncRNAs fell into the range of 200 bp to 300 bp, 343 lncRNAs were 300 bp to 400 bp, an […]


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PLEK institution(s)
School of Computer Science and Technology, Xidian University, XI'an, China; School of Computer Science and Engineering, XI'an University of Technology, XI'an, China; Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China

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