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Computer-Assisted Annotation of Small RNA Transcriptomes

  • Nicole Ortogero
  • Grant W. Hennig
  • Dickson Luong
  • Wei Yan
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1218)

Abstract

Small noncoding RNAs (sncRNAs) are widely expressed in the cell of almost all known species. Most sncRNAs appear to have regulatory roles, ranging from facilitating RNA production and modifications (e.g., snoRNAs) to control of mRNA stability and translational efficiency (e.g., miRNAs and endo-siRNA) and to transposon silencing (e.g., piRNAs). The affordability and efficiency of next-generation RNA deep sequencing (RNA-Seq) technologies have made sncRNA deep sequencing (sncRNA-Seq) analyses a routine in biomedical research. SncRNA-Seq analyses generate millions of reads and gigabytes of data; annotation of sncRNA-Seq data remains challenging due to a lack of comprehensive sncRNA annotation pipelines. To solve this problem, we have developed a computer-assisted sncRNA annotation pipeline, which uses open-source software and allows for not only proper classification of known sncRNAs, but also discovery of novel sncRNA species. In this chapter, we describe our sncRNA annotation protocol in detail.

Key words

Noncoding RNAs Next-generation sequencing High throughput Deep sequencing Software 

Notes

Acknowledgements

This work was supported by NIH grants (HD060858, HD071736, and HD074573) to W.Y. Software was developed in the Imaging Core (Core D) with support by the COBRE grant P20 RR-18751 from the NIH.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Nicole Ortogero
    • 1
  • Grant W. Hennig
    • 1
  • Dickson Luong
    • 1
  • Wei Yan
    • 1
  1. 1.Department of Physiology and Cell BiologyUniversity of Nevada School of MedicineRenoUSA

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