PLEK protocols

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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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  • person_outline Junying Zhang <>

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

PLEK in pipeline

2016
PMCID: 4931018
PMID: 27339440
DOI: 10.1038/ncomms11708

[…] long non-coding rnas (lncrnas) (mean length, 463 bp) were identified in maize by illumina short-read sequencing. to identify lncrnas in the pacbio data, we built a classification model using plek, trained on a high-confidence set of known non-coding rna genes. scanning of single-molecule long reads revealed 12,226 candidate lncrnas of ⩾200 bp. to obtain a high-confidence set of lncrna […]


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PLEK in publications

 (17)
PMCID: 5926538
PMID: 29690875
DOI: 10.1186/s12711-018-0391-0

[…] for coding potential using three different tools: cpat v1.2.3 [], which assigns coding probabilities to a given sequence based on differential hexamer usage [] and fickett testcode score [], plek v1.2, a support vector machine classifier using k-mer frequencies [], and cpc v0.9-r2 [], which was used in conjunction with the non-redundant sequence database, uniref90 (the uniref reference […]

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

[…] to identify potential lncrnas within the pool of unknown transcripts, four bioinformatic lncrna prediction tools were applied. the intersection of the alignment-free lncrna prediction tools (cnci, plek and feelnc) predicted 1,812 lncrna transcripts concordantly comprising a catalogue of 1,042 putative lncrna loci expressed in the calves’ intestinal mucosa., nine lncrna loci were differentially […]

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

[…] 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, […]

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

[…] genes and only kept the long (>200 bp) transcripts with no less than two exons. we then analyzed the protein-coding potential of the remaining transcripts using two computational tools: plek and cpat. the transcripts that were not predicted as protein coding by either of the two methods were retained as candidate lncrnas. the candidate lncrnas were merged with previous lncrnas […]

PMCID: 5664124
PMID: 29039813
DOI: 10.3390/genes8100274

[…] transcripts with fpkm scores <1, transcripts shorter than 200 nt, 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 […]


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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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