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piRNApredictor specifications

Information


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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  • person_outline Wen Zhang <>

Publications for piRNApredictor

piRNApredictor in publications

 (5)
PMCID: 4839659
PMID: 27101007
DOI: 10.1371/journal.pone.0154279

[…] 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., a test set of rnai-related proteins was created […]

PMCID: 4307313
PMID: 25580537
DOI: 10.3390/ijms16011466

[…] number of duplexes, mirplex primarily filters the sequences considered by abundance. this can lead to the omission of mirnas that were not highly expressed., for pirna, there exists a method, called pirnapredictor, for predicting mature pirna from small rna sequencing data []. pirnapredictor is based purely on nucleotide composition and does not require reference genomes nor sequencing […]

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

[…] these pirnas the most abundant were derived from unannotated sequences (table  ). in order 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 pirnapredictor output revealed more number of unique pirnas in each test sample (additional file : table s2). the output results […]

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

[…] as bm447, bm1770, bm1645 and sart1 []., the pirnas are generated mainly from germline cells and are specifically loaded onto germline-specific argonaute proteins-piwi proteins []. strangely, using pirnapredictor [] and an in-house developed perl script, a total of 54,033 reads were identified as pirna candidates among the te-derived small rna reads (table ), which accounted for 6.64% […]

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% ., the david functional annotation tool […]


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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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