RNA Type: Multiple classes
Overview: The RNA family database (Rfam) is a collection of RNA families represented by multiple sequence alignments, covariance models and profile Stochastic Context-Free Grammars.It stores information related to sequence, secondary structure, taxonomy, alignment and phylogenetic tree of different organisms.
Search Methods:
  • Similarity: search sequences against Rfam data. First, a pre-search with the program WU-BLAST is performed, followed by a secondary structural search using covariance models with the INFERNAL package.
  • Keyword: search by RNA family name, EMBL ID or accession number, ncRNA name/class, NCBI taxonomic classes.
  • Tabular: search by ID, accession, type, seed/full, average length, sequence identity and description (in Rfam families or families with 3D structures); by species, kingdom, families, region or genome size (in genomes search); ID, accession, number of families or description (in clans search); or by number of structures (in families with 3D structures.
Source: Literature, SRP, European ribosomal RNA database, 5S Ribosomal RNA database, RNase P database, uRNA database, tmRNA database.
Information Source: Experimental, In silico annotation, Literature, Manual curation.
Information Content: Alignment, Annotation, Covariance Model, Families of RNA, Sequence, Structure, Taxonomy.
Reference: Gardner et al., 2011; Gardner et al., 2009; Griffiths-Jones et al., 2005; Griffiths-Jones et al., 2003
PubmedID: 12520045, 15608160, 18945806, 18953034, 21062808.
Year: 2011;2009;2008;2005;2003
Multiple search: No
Download: GFF, Stockholm, FASTA, Other.
Genomic Overview: No
Organism: Arabidopsis Thaliana (Thale Cress), Brassica rapa, Glycine Max (Soybean), Medicago truncatula (Barrel Medic), Oryza sativa (Rice), Vitis vinifera, Carica papaya (Papaya), Ricinus communis (Castor bean), Lotus japonicus, Theobroma cacao (Cacao), Populus trichocarpa, Solanum lycopersicum (Tomato ), Brachypodium distachyon, Sorghum bicolor (Sorghum), Triticum aestivum (Bread wheat) and 261 others.

Url: http://rfam.sanger.ac.uk/
June 2018: Release 3.0