ViRome: An R package for the visualization and analysis of viral small RNA sequence datasets

Bioinformatics

Volumn 29, Issue 15, 2013, Pages 1902-1903

  Watson, Mick ^a   Schnettler, Esther ^b   Kohl, Alain ^b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b MRC UNIVERSITY OF GLASGOW CENTRE FOR VIRUS RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL UNTRANSLATED RNA; VIRUS RNA;

CHEMISTRY; COMPUTER GRAPHICS; COMPUTER PROGRAM; GENOMICS; RNA INTERFERENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; ARTICLE;

COMPUTER GRAPHICS; GENOMICS; RNA INTERFERENCE; RNA, SMALL UNTRANSLATED; RNA, VIRAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84880547557     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt297     Document Type: Article

References (17)

1. Antoniewski, C. (2011) Visitor, an informatic pipeline for analysis of viral siRNA sequencing datasets. Methods Mol. Biol., 721, 123-142.
2. Aravin, A.A. et al. (2003) The small RNA profile during Drosophila melanogaster development. Dev. Cell, 5, 337-350. (Pubitemid 37006476)
3. Bernstein, E. et al. (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363-366. (Pubitemid 32151243)
4. Blair, C.D. (2011) Mosquito RNAi is the major innate immune pathway controlling arbovirus infection and transmission. Future Microbiol., 6, 265-277.
5. Brennecke, J. et al. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 128, 1089-1103. (Pubitemid 46427877)
6. Donald, C.L. et al. (2012) New insights into control of arbovirus replication and spread by insect RNA interference pathways. Insects, 3, 511-531.
7. Fonseca, N.A. et al. (2012) Tools for mapping high-throughput sequencing data. Bioinformatics, 28, 3169-3177.
8. Gentleman, R.C. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
9. Lagos-Quintana, M. et al. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858. (Pubitemid 33032103)
10. Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
11. Morazzani, E.M. et al. (2012) Production of virus-derived ping-pong-dependent piRNA-like small RNAs in the mosquito soma. PLoS Pathog., 8, e1002470.
12. Myles, K.M. et al. (2009) Origins of alphavirus-derived small RNAs in mosquitoes. RNA Biol., 6, 387-391.
13. Sabin, L.R. et al. (2013) Dicer-2 processes diverse viral RNA species. PloS One, 8, e55458.
14. Schnettler, E. et al. (2013) RNA interference targets arbovirus replication in culi-coides cells. J. Virol., 87, 2441-2454.
15. Vodovar, N. et al. (2011) In silico reconstruction of viral genomes from small RNAs improves virus-derived small interfering RNA profiling. J. Virol., 85, 11016-11021.
16. Vodovar, N. et al. (2012) Arbovirus-derived piRNAs exhibit a ping-pong signature in mosquito cells. PloS One, 7, e30861.
17. Zamore, P.D. et al. (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101, 25-33. Council Council