Rfam

Rfam is an open access database, hosted at the Wellcome Trust Sanger Institute, containing information about RNA families. Designed to work in a similar way to its progenitor, the Pfam database of protein families, Rfam uses a similar model for annotation and display and is built on the same principle of open access to the data. The Rfam project is led at the Sanger Institute by Dr Paul Gardner and Dr Alex Bateman.

[Genome Research Limited]

Overview

Rfam contains information for RNA families and annotations for millions of RNA genes. Each entry in the Rfam database includes multiple sequence alignments, a secondary structure and probabilistic models known as covariance models, these models can simultaneously handle an RNA sequence and its structure.

RNA molecules act as messengers from the genome, containing instructions to build proteins; they act as structural components in the cell; they act to process molecules in the cell and they are fundamental in the regulation of cell activity. By building together information about RNAs, the Rfam project provides the research community with access to detailed information about these biologically important molecules in one unified location.

For each RNA family, the interface allows users to view and download multiple sequence alignments; read annotation; and examine species distribution of family members. Users can also access literature via the website and visit other RNA databases. Rfam recently launched a new community annotation system which allows users to edit or create Wikipedia entries linked from the Rfam website for RNAs stored in the database. The RNA families stored in Rfam are built by researchers at the Sanger Institute, often based on external sources.

RNAs housed in the database can be broadly divided into three categories non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. All of these classes of RNAs in the database are divided into families that share a common ancestor.

Rfam allows users to search the database by keyword, family name, or genome, also by entering a particular RNA sequence. Information held in the database is freely and openly available and can be downloaded or installed locally.

Selected Publications

  • Rfam: updates to the RNA families database.

    Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR and Bateman A

    Nucleic acids research 2009;37;Database issue;D136-40

    PUBMED: 18953034; PMC: 2686503; DOI: 10.1093/nar/gkn766

  • The RNA WikiProject: community annotation of RNA families.

    Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S and Bateman A

    RNA (New York, N.Y.) 2008;14;12;2462-4

    PUBMED: 18945806; PMC: 2590952; DOI: 10.1261/rna.1200508

  • Rfam: annotating non-coding RNAs in complete genomes.

    Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR and Bateman A

    Nucleic acids research 2005;33;Database issue;D121-4

    PUBMED: 15608160; PMC: 540035; DOI: 10.1093/nar/gki081

  • Rfam: an RNA family database.

    Griffiths-Jones S, Bateman A, Marshall M, Khanna A and Eddy SR

    Nucleic acids research 2003;31;1;439-41

    PUBMED: 12520045; PMC: 165453

* quick link - http://q.sanger.ac.uk/0b6c4q2v