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Prediction of piRNAs using transposon interaction and a support vector machine.

Wang K, Liang C, Liu J, Xiao H, Huang S, Xu J, Li F - BMC Bioinformatics (2014)

Bottom Line: Accurate prediction of piRNAs remains a significant challenge.As a result, 82,639 piRNAs were predicted in C. suppressalis.Piano demonstrates excellent piRNA prediction performance by using both structure and sequence features of transposon-piRNAs interactions.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China. wangk4@miamioh.edu.

ABSTRACT

Background: Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNA primarily expressed in germ cells that can silence transposons at the post-transcriptional level. Accurate prediction of piRNAs remains a significant challenge.

Results: We developed a program for piRNA annotation (Piano) using piRNA-transposon interaction information. We downloaded 13,848 Drosophila piRNAs and 261,500 Drosophila transposons. The piRNAs were aligned to transposons with a maximum of three mismatches. Then, piRNA-transposon interactions were predicted by RNAplex. Triplet elements combining structure and sequence information were extracted from piRNA-transposon matching/pairing duplexes. A support vector machine (SVM) was used on these triplet elements to classify real and pseudo piRNAs, achieving 95.3 ± 0.33% accuracy and 96.0 ± 0.5% sensitivity. The SVM classifier can be used to correctly predict human, mouse and rat piRNAs, with overall accuracy of 90.6%. We used Piano to predict piRNAs for the rice stem borer, Chilo suppressalis, an important rice insect pest that causes huge yield loss. As a result, 82,639 piRNAs were predicted in C. suppressalis.

Conclusions: Piano demonstrates excellent piRNA prediction performance by using both structure and sequence features of transposon-piRNAs interactions. Piano is freely available to the academic community at http://ento.njau.edu.cn/Piano.html .

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The length distribution of piRNAs in five species (D. melanogaster, C. suppressalis,R. norvegicus,M. musculus, andH. sapiens).
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Fig5: The length distribution of piRNAs in five species (D. melanogaster, C. suppressalis,R. norvegicus,M. musculus, andH. sapiens).

Mentions: Rice striped stem borer (SSB) is an important rice pest that causes huge yield loss. To date, no piRNAs have been reported in SSB. We applied our program to predict piRNAs from small RNA-Seq data; 2,170,655 short sequences in total. From this data, 82,639 piRNAs were predicted. The whole prediction procedure takes ~7 hours on an Ubuntu server (Sugon X8DT6, 2 CPU processors, each has 12 threads, 48 G memory). An interesting discovery is that insect piRNAs might have a different length distribution than mammalian piRNAs. The mammalian piRNAs have a length peak at 29–30 nt, whereas that in Drosophila is 24–26 nt and that in SSB is 27–28 nt (Figure 5). These findings are consistent with previous results [14].Figure 5


Prediction of piRNAs using transposon interaction and a support vector machine.

Wang K, Liang C, Liu J, Xiao H, Huang S, Xu J, Li F - BMC Bioinformatics (2014)

The length distribution of piRNAs in five species (D. melanogaster, C. suppressalis,R. norvegicus,M. musculus, andH. sapiens).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4308892&req=5

Fig5: The length distribution of piRNAs in five species (D. melanogaster, C. suppressalis,R. norvegicus,M. musculus, andH. sapiens).
Mentions: Rice striped stem borer (SSB) is an important rice pest that causes huge yield loss. To date, no piRNAs have been reported in SSB. We applied our program to predict piRNAs from small RNA-Seq data; 2,170,655 short sequences in total. From this data, 82,639 piRNAs were predicted. The whole prediction procedure takes ~7 hours on an Ubuntu server (Sugon X8DT6, 2 CPU processors, each has 12 threads, 48 G memory). An interesting discovery is that insect piRNAs might have a different length distribution than mammalian piRNAs. The mammalian piRNAs have a length peak at 29–30 nt, whereas that in Drosophila is 24–26 nt and that in SSB is 27–28 nt (Figure 5). These findings are consistent with previous results [14].Figure 5

Bottom Line: Accurate prediction of piRNAs remains a significant challenge.As a result, 82,639 piRNAs were predicted in C. suppressalis.Piano demonstrates excellent piRNA prediction performance by using both structure and sequence features of transposon-piRNAs interactions.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China. wangk4@miamioh.edu.

ABSTRACT

Background: Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNA primarily expressed in germ cells that can silence transposons at the post-transcriptional level. Accurate prediction of piRNAs remains a significant challenge.

Results: We developed a program for piRNA annotation (Piano) using piRNA-transposon interaction information. We downloaded 13,848 Drosophila piRNAs and 261,500 Drosophila transposons. The piRNAs were aligned to transposons with a maximum of three mismatches. Then, piRNA-transposon interactions were predicted by RNAplex. Triplet elements combining structure and sequence information were extracted from piRNA-transposon matching/pairing duplexes. A support vector machine (SVM) was used on these triplet elements to classify real and pseudo piRNAs, achieving 95.3 ± 0.33% accuracy and 96.0 ± 0.5% sensitivity. The SVM classifier can be used to correctly predict human, mouse and rat piRNAs, with overall accuracy of 90.6%. We used Piano to predict piRNAs for the rice stem borer, Chilo suppressalis, an important rice insect pest that causes huge yield loss. As a result, 82,639 piRNAs were predicted in C. suppressalis.

Conclusions: Piano demonstrates excellent piRNA prediction performance by using both structure and sequence features of transposon-piRNAs interactions. Piano is freely available to the academic community at http://ento.njau.edu.cn/Piano.html .

Show MeSH
Related in: MedlinePlus