Pathogen detection using short-RNA deep sequencing subtraction and assembly

Bioinformatics

Volumn 27, Issue 15, 2011, Pages 2027-2030

  Isakov, Ofer ^a   Modai, Shira ^a   Shomron, Noam ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

BACTERIAL RNA; VIRUS RNA;

ARTICLE; CELL LINE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; METHODOLOGY; MYCOPLASMA; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

CELL LINE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV; HUMANS; MYCOPLASMA; RNA, BACTERIAL; RNA, VIRAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 79960417564     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr349     Document Type: Article

References (17)

1. Briese,T. et al. (2009) Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated Arenavirus from Southern Africa. PLoS Pathogens, 5, e1000455.
2. Douglas,R. (2005) Challenges and opportunities for pathogen detection using DNA microarrays. Crit. Rev. Microbiol., 31, 91-99.
3. Dumontier,M. and Hogue,C.W. (2002) NBLAST: a cluster variant of BLAST for NxN comparisons. BMC Bioinformatics, 3, 13.
4. Kreuze,J.F. et al. (2009) Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology, 388, 1-7.
5. Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
6. MacConaill,L. and Meyerson,M. (2008) Adding pathogens by genomic subtraction. Nat. Genet., 40, 380-382.
7. Obbard,D.J. et al. (2009) The evolution of RNAi as a defence against viruses and transposable elements. Philos. Trans. R. Soc. Lond. B Biol. Sci., 364, 99-115.
8. Rauhut,R. and Klug,G. (1999) mRNA degradation in bacteria. FEMS Microbiol. Rev., 23, 353-370.
9. Straub,T.M. et al. (2005) Automated methods for multiplexed pathogen detection. J. Microbiol. Methods, 62, 303-316.
10. Trapnell,C. and Salzberg,S.L. (2009a) How tomap billions of short reads onto genomes. Nat. Biotechnol., 27, 455-457.
11. Trapnell,C. et al. (2009b) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
12. Voelkerding,K.V. et al. (2009) Next-generation sequencing: from basic research to diagnostics. Clin. Chem., 55, 641-658.
13. Wang,C. et al. (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res., 17, 1195-1201.
14. Weber,G. et al. (2002) Identification of foreign gene sequences by transcript filtering against the human genome. Nat. Genet., 30, 141-142.
15. Wu,Q. et al. (2010) Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs. Proc. Natl Acad. Sci. USA, 107, 1606-1611.
16. Xu,Y. et al. (2003) Pathogen discovery from human tissue by sequence-based computational subtraction. Genomics. 81, 329-335.
17. Zerbino,D.R. and Birney,E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.