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Rfam: updates to the RNA families database.

TitleRfam: updates to the RNA families database.
Publication TypeJournal Article
Year of Publication2009
AuthorsGardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A
JournalNucleic Acids Res
Volume37
IssueDatabase issue
PaginationD136-40
Date Published2009 Jan
ISSN1362-4962
KeywordsComputer Graphics, Databases, Nucleic Acid, Internet, RNA, Sequence Alignment, Sequence Analysis, RNA
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/.

DOI10.1093/nar/gkn766
Alternate JournalNucleic Acids Res.
PubMed ID18953034
PubMed Central IDPMC2686503
Grant List077044 / / Wellcome Trust / United Kingdom
/ / Howard Hughes Medical Institute / United States
/ / Wellcome Trust / United Kingdom