Rfam: Updates to the RNA families database

Paul P. Gardner; Jennifer Daub; John G. Tate; Eric P. Nawrocki; Diana L. Kolbe; Stinus Lindgreen; Adam C. Wilkinson; Robert D. Finn; Sam Griffiths-Jones; Sean R. Eddy; Alex Bateman

doi:10.1093/nar/gkn766

Rfam: Updates to the RNA families database

Paul P. Gardner, Jennifer Daub, John G. Tate, Eric P. Nawrocki, Diana L. Kolbe, Stinus Lindgreen, Adam C. Wilkinson, Robert D. Finn, Sam Griffiths-Jones, Sean R. Eddy, Alex Bateman

Research output: Contribution to journal › Article › peer-review

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/. © 2008 The Author(s).

Original language	English
Pages (from-to)	D136-D140
Journal	Nucleic acids research.
Volume	37
Issue number	1
DOIs	https://doi.org/10.1093/nar/gkn766
Publication status	Published - 2009

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title = "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/. {\textcopyright} 2008 The Author(s).",

author = "Gardner, {Paul P.} and Jennifer Daub and Tate, {John G.} and Nawrocki, {Eric P.} and Kolbe, {Diana L.} and Stinus Lindgreen and Wilkinson, {Adam C.} and Finn, {Robert D.} and Sam Griffiths-Jones and Eddy, {Sean R.} and Alex Bateman",

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doi = "10.1093/nar/gkn766",

language = "English",

volume = "37",

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TY - JOUR

T1 - Rfam: Updates to the RNA families database

AU - Gardner, Paul P.

AU - Daub, Jennifer

AU - Tate, John G.

AU - Nawrocki, Eric P.

AU - Kolbe, Diana L.

AU - Lindgreen, Stinus

AU - Wilkinson, Adam C.

AU - Finn, Robert D.

AU - Griffiths-Jones, Sam

AU - Eddy, Sean R.

AU - Bateman, Alex

PY - 2009

Y1 - 2009

N2 - 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/. © 2008 The Author(s).

AB - 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/. © 2008 The Author(s).

U2 - 10.1093/nar/gkn766

DO - 10.1093/nar/gkn766

M3 - Article

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SN - 1362-4962

VL - 37

SP - D136-D140

JO - Nucleic acids research.

JF - Nucleic acids research.

IS - 1

ER -

Rfam: Updates to the RNA families database

Abstract

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