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Piano specifications

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Unique identifier OMICS_20434
Name Piano
Alternative name piRNA annotation
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Some small RNA data.
Input format FASTA
Operating system Unix/Linux
Programming languages Shell (Bash)
Computer skills Advanced
Stability Stable
Requirements
Seqmap, RNAplex, LIBSVM
Maintained Yes

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Maintainers


  • person_outline Kai
  • person_outline Fei Li

Publication for piRNA annotation

Piano citations

 (5)
library_books

Computational methods reveal novel functionalities of PIWI interacting RNAs in human papillomavirus induced head and neck squamous cell carcinoma

2017
Oncotarget
PMCID: 5797000
PMID: 29435129
DOI: 10.18632/oncotarget.23464

[…] piRNA read counts were generated from sequencing datasets via BEDtools coverageBed (https://github.com/arq5x/bedtools2) using piRNA annotation files. The piRNA BED file containing 27,127 piRNA transcripts was obtained from NONCODEv4 (http://www.bioinfo.org/NONCODEv4/), a database integrating ncRNA data from RefSeq, Ensembl, […]

library_books

The downregulation of putative anticancer target BORIS/CTCFL in an addicted myeloid cancer cell line modulates the expression of multiple protein coding and ncRNA genes

2017
Oncotarget
PMCID: 5650274
PMID: 29088719
DOI: 10.18632/oncotarget.20627

[…] with the Dicer cleavage site and the minimum free energy were analyzed via miRDeep2 []. Target prediction analysis with GO enrichment and KEGG [] pathway analysis were made.For piRNA prediction, the Piano [] tool was used. To discover potential piRNAs [], their structural features (namely, the fact, that each strand of this 22-24nt long dual-strand RNA is 2nt longer on the 3’ end than the paired […]

library_books

snoRNA and piRNA expression levels modified by tobacco use in women with lung adenocarcinoma

2017
PLoS One
PMCID: 5560661
PMID: 28817650
DOI: 10.1371/journal.pone.0183410

[…] d to FASTQ using BEDtools []. Converted files were aligned to the human genome using Novoalign with the same configuration as described above, aiming for the detection of sncRNAs other than miRNA.The piRNA annotation file was obtained from the piRNAbank database [], and overlapping annotations that were in the same orientation were grouped into clusters (). This modified GTF file has 2,049 piRNA c […]

library_books

ALG 5 is a miRNA associated Argonaute required for proper developmental timing in the Caenorhabditis elegans germline

2017
Nucleic Acids Res
PMCID: 5587817
PMID: 28645154
DOI: 10.1093/nar/gkx536

[…] erl and Python scripts. miRNA annotation was based on miRBase release 20. Mutator class siRNA annotation was based on Phillips et al. (). CSR-1 class siRNA annotation was based on Claycomb et al. (). piRNA annotation was based on WormBase release WS230. New miRNAs were identified using miRDeep2 (). To identify GFP::ALG-5, HA::ALG-5, HA::ALG-1 and HA::ALG-2 interactors, we calculated the normalized […]

library_books

The non coding landscape of head and neck squamous cell carcinoma

2016
Oncotarget
PMCID: 5239470
PMID: 27323410
DOI: 10.18632/oncotarget.9979

[…] from the TCGA Level 3 gene expression analyses. lncRNA and piRNA read counts were generated from sequencing datasets via BEDtools coverageBed (https://github.com/arq5x/bedtools2) [] using lncRNA and piRNA annotation files. A lncRNA BED file containing 113,438 transcripts was obtained from LNCipedia 3.0 (http://lncipedia.org/) [], a database curating lncRNAs from sources including the Broad Instit […]

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Piano institution(s)
Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Department of Biology, Miami University, Oxford, OH, USA; Department of Computer Science and software Engineering, Miami University, Oxford, OH, USA; College of Information and Technology, Nanjing Agricultural University, Nanjing, China; College of computer science and Technology, Nanjing Normal University, Nanjing, China

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