Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Aug 1;27(15):2027-30.
doi: 10.1093/bioinformatics/btr349. Epub 2011 Jun 11.

Pathogen detection using short-RNA deep sequencing subtraction and assembly

Ofer Isakov  1 , Shira Modai, Noam Shomron
Affiliations

Pathogen detection using short-RNA deep sequencing subtraction and assembly

Ofer Isakov et al. Bioinformatics. .

Abstract

Early and accurate detection of human pathogen infection is critical for treatment and therapeutics. Here we describe pathogen identification using short RNA subtraction and assembly (SRSA), a detection method that overcomes the requirement of prior knowledge and culturing of pathogens, by using degraded small RNA and deep sequencing technology. We prove our approach's efficiency through identification of a combined viral and bacterial infection in human cells.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
PCR products visualized in 1.5% agarose gel, a single band for both SupT1 + HIV-1 sample (lane 4) and the positive control (c) from the mycoplasma detection kit (lane 2) observed within the predicted marker (m) size range (270 bp). Lane 3 is the uninfected cells.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Briese T., et al. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever–associated Arenavirus from Southern Africa. PLoS Pathogens. 2009;5:e1000455. - PMC - PubMed
    1. Douglas R. Challenges and opportunities for pathogen detection using DNA microarrays. Crit. Rev. Microbiol. 2005;31:91–99. - PubMed
    1. Dumontier M., Hogue C.W. NBLAST: a cluster variant of BLAST for NxN comparisons. BMC Bioinformatics. 2002;3:13. - PMC - PubMed
    1. Kreuze J.F., et al. 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. 2009;388:1–7. - PubMed
    1. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;26:589–595. - PMC - PubMed

Publication types