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Number of citations per year for the bioinformatics software tool piRNApredictor
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This map represents all the scientific publications referring to piRNApredictor per scientific context
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Protocols

piRNApredictor specifications

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Unique identifier OMICS_20431
Name piRNApredictor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Wen Zhang

Publications for piRNApredictor

piRNApredictor citations

 (6)
library_books

qiRNApredictor: A Novel Computational Program for the Prediction of qiRNAs in Neurospora crassa

2016
PLoS One
PMCID: 4948831
PMID: 27428111
DOI: 10.1371/journal.pone.0159487

[…] el for piRNA prediction []. In 2011, Zhang et al. used a simple k-mer scheme to construct 1364 dimension feature vectors for describing the candidate piRNA sequences and then constructed the software piRNApredictor for piRNA prediction based on an improved Fisher linear algorithm []. Moreover, position-specific scoring matrix (PSSM) is a commonly used representation of sequence motifs, which has b […]

call_split

Characterization of the Small RNA Transcriptome of the Marine Coccolithophorid, Emiliania huxleyi

2016
PLoS One
PMCID: 4839659
PMID: 27101007
DOI: 10.1371/journal.pone.0154279
call_split See protocol

[…] quence reads between 26–30 nt in the smRNA library were compared using BLASTN to the known human and rat piRNAs housed in piRNABank []. Because piRNAs exhibit little sequence homology across species, piRNApredictor, a k-mer scheme which employs a Fisher Disciminant algorithm with greater than 90% precision and 60% sensitivity [], was also used. […]

library_books

Prediction of Mature MicroRNA and Piwi Interacting RNA without a Genome Reference or Precursors

2015
Int J Mol Sci
PMCID: 4307313
PMID: 25580537
DOI: 10.3390/ijms16011466

[…] rue positive rate compared to the standard L2-based Gaussian kernel. Analysis of the hold-out test set shows that our approach can increase the true positive rate for piRNA by at most 60% compared to piRNApredictor. Finally, we show that our approach can detect about an order of magnitude or more of the known miRNAs than miRPlex using experimental datasets.In the future, we plan to study the possi […]

library_books

Small non coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells

2014
BMC Genomics
PMCID: 4286946
PMID: 25185950
DOI: 10.1186/1471-2164-15-757

[…] cance level of p ≤ 0.05 for increased hit density, and a minimum score of 1.3 for strand bias). To cross-validate the putative chicken piRNAs, we performed another ab initio predictive analysis using piRNApredictor software [] with the sequence reads of test samples. The output results of proTRAC and piRNApredictor were then compared to control the false positive rate. […]

library_books

RIP seq of BmAgo2 associated small RNAs reveal various types of small non coding RNAs in the silkworm, Bombyx mori

2013
BMC Genomics
PMCID: 3849828
PMID: 24074203
DOI: 10.1186/1471-2164-14-661

[…] eads were then used to predict the novel miRNAs and to base edit the potential known miRNAs. The >25nt TE-derived small RNAs and remaining unannotated reads were selected for probing piRNAs using the piRNApredictor program [] and Perl script developed by us. The reads that perfectly mapped to the BmNPV genome were used to predict the BmNPV-encoded miRNAs using mirExplorer software []. Finally, the […]

library_books

Discovery of Potential piRNAs from Next Generation Sequences of the Sexually Mature Porcine Testes

2012
PLoS One
PMCID: 3321025
PMID: 22493715
DOI: 10.1371/journal.pone.0034770

[…] those that gave hits for genic regions (exons) were classified as “gene”. We classified the remaining small RNAs as “no annotation”. Small RNAs ≥ 26 nt were used to predict piRNA sequences by online piRNApredictor software (http://59.79.168.90/piRNA/analysis.php), a novel ‘dynamic’ algorithm with a precision of over 90% and a sensitivity of over 60% . […]


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piRNApredictor institution(s)
School of Mathematics and Statistics, Wuhan University, Wuhan, China; State Key Lab of Software Engineering, Wuhan University, Wuhan, China; School of Computer, Wuhan University, Wuhan, China; International School of Software, Wuhan University, Wuhan, China
piRNApredictor funding source(s)
Supported by the National Natural Science Foundation of China (61103126, 61271337, 61402340 and 61572368), Shenzhen Development Foundation (JCYJ20130401160028781) and Natural Science Foundation of Hubei Province of China (2014CFB194).

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