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Rfam
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
