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

Functional Genomics

625 Citations (Scopus)

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/.

Original language	English
Journal	Nucleic Acids Research
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gkn766
Publication status	Published - 2008

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10.1093/nar/gkn766

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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/.",

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",

year = "2008",

doi = "10.1093/nar/gkn766",

language = "English",

journal = "Nucleic Acids Research",

issn = "0305-1048",

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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 - 2008

Y1 - 2008

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/.

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/.

U2 - 10.1093/nar/gkn766

DO - 10.1093/nar/gkn766

M3 - Journal article

C2 - 18953034

SN - 0305-1048

JO - Nucleic Acids Research

JF - Nucleic Acids Research

ER -

Rfam: updates to the RNA families database

Abstract

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