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Rfam: updates to the RNA families database.

ABSTRACT: Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited taxonomic range and provide a limited number of annotations. Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/.

SUBMITTER: Gardner PP

PROVIDER: S-EPMC2686503 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature

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Rfam: updates to the RNA families database.

Gardner Paul P PP Daub Jennifer J Tate John G JG Nawrocki Eric P EP Kolbe Diana L DL Lindgreen Stinus S Wilkinson Adam C AC Finn Robert D RD Griffiths-Jones Sam S Eddy Sean R SR Bateman Alex A

Nucleic acids research 20081025 Database issue

Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have ...[more]

PMID: 18953034

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