The Rfam database is a collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements. Each family is represented by a multiple sequence alignment and a covariance model (CM).
You can use the Rfam website to obtain information about an individual family, or browse the families and genome annotations. Alternatively you can download all of the Rfam data from the FTP site. Find out more about the project by exploring the latest :ref:`citing-rfam:Rfam references`.
For each family Rfam provides:
- Summary page
- Textual background information on the RNA family, which we obtain from the online encyclopedia Wikipedia
- Seed alignment
- A curated alignment containing a small set of representative sequences and a consensus secondary structure annotation
- Information about sequences in the family, including bit score, seed and full alignments, region coordinates, sequence description from the EMBL nucleotide database, and the species name
- Secondary structure
- Secondary structure images, annotated with various measures of sequence and structure conservation
- Interactive tree graphic displaying species distribution for the full alignment.
- Phylogenetic trees are available for the seed and the full alignment
- Mappings between PDB structures and Rfam annotations
- Database references
- Links to external databases and references to other data sources
- Covariance model files contain information summarising the family, including the author of alignment, references for sources of sequence and/or structure, the number of sequences in each alignment, score thresholds and score distributions