Rfam: updates to the RNA families database

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/.

[1]  Wayne A. Decatur,et al.  New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. , 2007, RNA.

[2]  Laurent Lestrade,et al.  snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs , 2005, Nucleic Acids Res..

[3]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[4]  Elena Rivas,et al.  Probabilistic Phylogenetic Inference with Insertions and Deletions , 2008, PLoS Comput. Biol..

[5]  Chris M. Brown,et al.  Transterm—extended search facilities and improved integration with other databases , 2005, Nucleic Acids Res..

[6]  P. Stadler,et al.  Secondary structure prediction for aligned RNA sequences. , 2002, Journal of molecular biology.

[7]  C. Chothia,et al.  Volume changes in protein evolution. , 1994, Journal of molecular biology.

[8]  J. Tate,et al.  The RNA WikiProject: community annotation of RNA families. , 2008, RNA.

[9]  Paul D. Shaw,et al.  Plant snoRNA database , 2003, Nucleic Acids Res..

[10]  David Haussler,et al.  Identification and Classification of Conserved RNA Secondary Structures in the Human Genome , 2006, PLoS Comput. Biol..

[11]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[12]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[13]  Martin Mokrejs,et al.  IRESite: the database of experimentally verified IRES structures () , 2005, Nucleic Acids Res..

[14]  Elena Rivas,et al.  Noncoding RNA gene detection using comparative sequence analysis , 2001, BMC Bioinformatics.

[15]  Jonathan P. Bollback,et al.  Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. , 2006, Genome research.

[16]  J. Vogel,et al.  Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq , 2008, PLoS genetics.

[17]  Ivo L. Hofacker,et al.  The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures , 2007, Nucleic Acids Res..

[18]  F. H. D. van Batenburg,et al.  PseudoBase: structural information on RNA pseudoknots , 2001, Nucleic Acids Res..

[19]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[20]  I. Hofacker,et al.  Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. , 2004, Journal of molecular biology.

[21]  Dan Wu,et al.  Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database , 2007, Nucleic Acids Res..

[22]  Sean R. Eddy,et al.  Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..

[23]  Sean R. Eddy,et al.  Query-Dependent Banding (QDB) for Faster RNA Similarity Searches , 2007, PLoS Comput. Biol..

[24]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[25]  Hagen Blankenburg,et al.  Integrating biological data – the Distributed Annotation System , 2008, BMC Bioinformatics.

[26]  Peter F Stadler,et al.  Fast and reliable prediction of noncoding RNAs , 2005, Proc. Natl. Acad. Sci. USA.