Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Rfam: annotating non-coding RNAs in complete genomes.

Sam Griffiths-Jones1, Simon Moxon, Mhairi Marshall

  • 1The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. sgj@sanger.ac.uk

Nucleic Acids Research
|December 21, 2004
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins.

Bioinformatics advances·2026
Same author

RNA Folding Energy of Long-Range Genomic Interactions Regulates Discontinuous Transcription in SARS-CoV-2.

Viruses·2026
Same author

InterProScan 6: a modern large-scale protein function annotation pipeline.

Bioinformatics advances·2026
Same author

Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT.

bioRxiv : the preprint server for biology·2026
Same author

HMMER web server: 2026 update.

Nucleic acids research·2026
Same author

Cytomegalovirus-specific CD154-expressing T Cells are Present Before Transplantation in Cytomegalovirus-seronegative Recipients and Predict Early Cytomegalovirus DNAemia.

Transplantation direct·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Epigenetic landscape of synthetic human centromere core regions: CENP-A assembly and euchromatic modifications interdependently antagonize heterochromatin accumulation.

Nucleic acids research·2026
Same journal

MAPK/ERK signaling regulates H3K9me3 heterochromatin reorganization to confer mesendoderm developmental competence.

Nucleic acids research·2026
See all related articles

Rfam is a comprehensive database of non-coding RNA (ncRNA) families, aiding in the identification and classification of new ncRNAs. It reveals conserved ncRNA families across life, with some essential universally and others taxon-specific.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Non-coding RNAs (ncRNAs) play crucial roles in various biological processes.
  • Identifying and classifying ncRNA families is essential for understanding genome function.
  • Existing databases may lack comprehensive coverage or up-to-date annotations.

Purpose of the Study:

  • To present Rfam, a curated database of ncRNA families.
  • To facilitate the identification and classification of novel ncRNA members.
  • To provide genome-wide annotations of ncRNAs.

Main Methods:

  • Utilizing multiple sequence alignments to represent ncRNA families.
  • Employing profile stochastic context-free grammars for ncRNA modeling.
  • Distributing ncRNA annotations across over 200 complete genomes.

Related Experiment Videos

Main Results:

  • Rfam provides a comprehensive collection of ncRNA families.
  • The database enables the identification of new members within known families.
  • Analysis reveals conservation of ncRNA families across diverse taxa.
  • A subset of large ncRNA families is conserved across all three domains of life.
  • Numerous smaller ncRNA families exhibit taxonomic specificity.

Conclusions:

  • Rfam serves as a valuable resource for ncRNA research.
  • The database highlights the evolutionary conservation and diversification of ncRNAs.
  • Future improvements and challenges for Rfam are discussed.