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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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Rfam: annotating families of non-coding RNA sequences.

Jennifer Daub1, Ruth Y Eberhardt, John G Tate

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK, jd7@sanger.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)
|January 12, 2015
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Summary

The Rfam database collects and organizes noncoding RNA (ncRNA) sequences, aiding in the identification and annotation of homologous sequences using curated families and clans.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Noncoding RNAs (ncRNAs) play crucial roles in gene regulation and cellular processes.
  • Accurate identification and annotation of ncRNA sequences are essential for understanding their functions.
  • Existing databases often lack comprehensive, manually curated collections of validated ncRNA data.

Purpose of the Study:

  • To present the Rfam database as a centralized resource for experimentally validated noncoding RNA (ncRNA) sequences.
  • To facilitate the prediction and annotation of novel ncRNA homologues in newly sequenced genomes.
  • To provide researchers with tools for searching, browsing, and annotating sequences using Rfam's curated families and clans.

Main Methods:

  • Collating experimentally validated ncRNA sequences from published literature.
  • Grouping homologous ncRNA sequences into families and related families into clans.
  • Manually curating data cross-references from other databases and external resources.
  • Developing covariance models (CMs) for sequence annotation.
  • Providing a web interface with tools for searching, browsing, and downloading Rfam data.

Main Results:

  • Rfam successfully collates and organizes a vast collection of validated ncRNA sequences.
  • The database provides a structured classification of ncRNAs into families and clans.
  • Rfam offers robust tools for annotating novel sequences and retrieving comprehensive family information.
  • The manual curation process ensures high-quality, reliable data for researchers.

Conclusions:

  • Rfam serves as a vital, high-quality resource for the ncRNA research community.
  • The database significantly aids in the discovery and functional annotation of ncRNAs.
  • Rfam's tools empower researchers to integrate ncRNA analysis into their own studies effectively.