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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Predicting RNA Families in Nucleotide Sequences Using StructRNAfinder.

Vinicius Maracaja-Coutinho1,2,3, Raúl Arias-Carrasco4,5, Helder I Nakaya6

  • 1Facultad de Ciencias Químicas y Farmacéuticas, Advanced Center for Chronic Diseases-ACCDiS, Universidad de Chile, Santiago, Chile. vinicius.maracaja@uchile.cl.

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StructRNAfinder simplifies noncoding RNA (ncRNA) family identification and annotation. This automated tool aids researchers in predicting RNA families from genomic or transcriptomic sequences.

Keywords:
Covariance modelsGene predictionsNoncoding RNAsRNA familiesRNA prediction

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Area of Science:

  • Genomics and transcriptomics
  • Bioinformatics
  • Computational biology

Background:

  • Noncoding RNAs (ncRNAs) are crucial regulatory molecules identified through genomics and transcriptomics.
  • Covariance models (CMs) are sensitive for ncRNA family prediction but require multiple tools, posing challenges for researchers.
  • Existing workflows for large-scale ncRNA prediction and annotation are complex and computationally intensive.

Purpose of the Study:

  • To introduce StructRNAfinder, an automated tool for the identification and annotation of regulatory RNA families.
  • To provide a comprehensive tutorial for utilizing both stand-alone and web server versions of StructRNAfinder.
  • To enable researchers, regardless of their computational background, to predict ncRNA families from sequence data.

Main Methods:

  • Development of an automated pipeline for ncRNA family identification and annotation.
  • Implementation of StructRNAfinder as both a stand-alone software and a web server.
  • Detailed tutorial covering installation and prediction procedures for diverse sequence datasets.

Main Results:

  • StructRNAfinder automates the identification and annotation of ncRNA families directly from nucleotide sequences.
  • The tool supports predictions across various genomic and transcriptomic datasets.
  • User-friendly tutorials facilitate the adoption and application of StructRNAfinder.

Conclusions:

  • StructRNAfinder overcomes the complexity of traditional ncRNA analysis pipelines.
  • The tool empowers researchers to perform large-scale ncRNA predictions and annotations efficiently.
  • StructRNAfinder enhances accessibility to ncRNA research for a broader scientific community.