NcPRO-seq: A tool for annotation and profiling of ncRNAs in sRNA-seq data

Bioinformatics

Volumn 28, Issue 23, 2012, Pages 3147-3149

  Chen, Chong Jian ^a,b,c,d   Servant, Nicolas ^a,c,d   Toedling, Joern ^a,b,c,d,e   Sarazin, Alexis ^f   Marchais, Antonin ^g   Duvernois Berthet, Evelyne ^f   Cognat, Valérie ^h   Colot, Vincent ^f   Voinnet, Olivier ^g   Heard, Edith ^a,b   Ciaudo, Constance ^a,b,g   Barillot, Emmanuel ^a,c,d  

^a INSTITUT CURIE   (France)

^b INSTITUT CURIE   (France)

^c INSERM U900   (France)

^d PSL RESEARCH UNIVERSITY   (France)

^e Institute of Molecular Biology GGmbH   (Germany)

^f PSL RESEARCH UNIVERSITY   (France)

^g ETH ZURICH   (Switzerland)

^h UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALIA;

SMALL INTERFERING RNA; UNTRANSLATED RNA;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENETICS; INTERNET; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; INTERNET; RNA, SMALL INTERFERING; RNA, UNTRANSLATED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84870420933     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts587     Document Type: Article

References (22)

1. Brodersen, P. and Voinnet, O. (2006) The diversity of RNA silencing pathways in plants. Trends Genet., 22, 268-280.
2. Clark, M.B. et al. (2011) The reality of pervasive transcription. PLoS Biol., 9, e1000625; discussion e1001102.
3. Cole, C. et al. (2009) Filtering of deep sequencing data reveals the existence of abundant dicer-dependent small RNAs derived from tRNAs. RNA, 15, 2147-2160.
4. Dreszer, T.R. et al. (2012) The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res., 40, D918-D923.
5. Fasold, M. et al. (2011) DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res., 39, W112-W117.
6. Gardner, P.P. et al. (2011) Rfam: Wikipedia, clans and the 'decimal' release. Nucleic Acids Res., 39, D141-D145.
7. Ghildiyal, M. and Zamore, P. (2009) Small silencing RNAs: an expanding universe. Nat. Rev. Genet., 10, 94-108.
8. Hackenberg, M. et al. (2011) miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res., 39, W132-W138.
9. Hardcastle, T. et al. (2012) Identifying small interfering RNA loci from high-throughput sequencing data. Bioinformatics, 28, 457-463.
10. Kim, T.K. et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature, 465, 182-187.
11. Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
12. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
13. MacLean, D. et al. (2010) Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics, 11, 93.
14. Pantano, L. et al. (2011) A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome. Bioinformatics, 27, 3202-3203.
15. Pederson, T. (2010) Regulatory RNAs derived from transfer RNA? RNA, 16, 1865-1869.
16. Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
17. Rajagopalan, R. et al. (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev., 20, 3407-3425.
18. Ronen, R. et al. (2010) miRNAkey: a software for microRNA deep sequencing analysis. Bioinformatics, 26, 2615-2616.
19. Stocks, M. et al. (2012) The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets. Bioinformatics, 28, 2059-2061.
20. Taft, R.J. et al. (2009) Small RNAs derived from snoRNAs. RNA, 15, 1233-1240.
21. Taft, R.J. et al. (2010) Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat. Struct. Mol. Biol., 17, 1030-1034.
22. Toedling, J. et al. (2010) Girafe-an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. Bioinformatics, 26, 2902-2903.