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Predicting RNA Families in Nucleotide Sequences Using StructRNAfinder

  • Vinicius Maracaja-CoutinhoEmail author
  • Raúl Arias-Carrasco
  • Helder I. Nakaya
  • Victor Aliaga-Tobar
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1962)

Abstract

Noncoding RNA (ncRNA) research is already a routine in every genomics or transcriptomics initiatives. According to their functions, ncRNAs can be grouped into several different RNA families, which can be represented by conserved primary sequences, secondary structures, or covariance models (CMs). CMs are very sensitive in predicting RNA families in nucleotide sequences and have been widely used in characterizing the repertoire of ncRNAs in organisms from all domains of life. However, the large-scale prediction and annotation of ncRNAs require multiple tools along the process, imposing a great obstacle for researchers with lesser computational or bioinformatics background. StructRNAfinder emerged as an automated tool to avoid these bottlenecks, by performing the automatic identification and complete annotation of regulatory RNA families derived directly from nucleotide sequences. In this chapter, we provide a complete tutorial for both stand-alone and web server versions of StructRNAfinder. This will help users to install the tool and to perform predictions of RNA families in any genome or transcriptome sequences dataset.

Key words

RNA families RNA prediction Noncoding RNAs Covariance models Gene predictions 

Notes

Acknowledgments

VMC was funded by grants from Comisión Nacional de Investigación Científica y Tecnológica (CONICYT): grants FONDECYT (11161020), PAI (PAI79170021), and FONDAP (15130011), Chile. RAC and VAT received a fellowship from Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, Santiago, Chile. HIN received grants from Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), Brazil: 2012/19278-6 and 2017/50137-3.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Vinicius Maracaja-Coutinho
    • 1
    • 2
    • 3
    Email author
  • Raúl Arias-Carrasco
    • 1
    • 4
  • Helder I. Nakaya
    • 5
  • Victor Aliaga-Tobar
    • 1
    • 4
  1. 1.Facultad de Ciencias Químicas y Farmacéuticas, Advanced Center for Chronic Diseases—ACCDiSUniversidad de ChileSantiagoChile
  2. 2.Beagle BioinformaticsSantiagoChile
  3. 3.Instituto VandiqueJoão PessoaBrazil
  4. 4.Programa de Doctorado en Genómica Integrativa, Vicerrectoría de InvestigaciónUniversidad MayorSantiagoChile
  5. 5.Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of São PauloSão PauloBrazil

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