Rfam: updates to the RNA families database
Top Cited Papers
Open Access
- 25 October 2008
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 37 (Database), D136-D140
- https://doi.org/10.1093/nar/gkn766
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/.Keywords
This publication has 26 references indexed in Scilit:
- The RNA WikiProject: Community annotation of RNA familiesRNA, 2008
- Probabilistic Phylogenetic Inference with Insertions and DeletionsPLoS Computational Biology, 2008
- Integrating biological data – the Distributed Annotation SystemBMC Bioinformatics, 2008
- Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence DatabaseNucleic Acids Research, 2007
- miRBase: tools for microRNA genomicsNucleic Acids Research, 2007
- The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structuresNucleic Acids Research, 2007
- New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNARNA, 2007
- Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNAGenome Research, 2006
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002
- The Protein Data BankNucleic Acids Research, 2000