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Rfam

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Rfam is a database containing information about non-coding RNA ncRNA families and other structured RNA elements It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute Rfam is designed to be similar to the Pfam database for annotating protein families

Unlike proteins, ncRNAs often have similar secondary structure without sharing much similarity in the primary sequence Rfam divides ncRNAs into families based on evolution from a common ancestor Producing multiple sequence alignments MSA of these families can provide insight into their structure and function, similar to the case of protein families These MSAs become more useful with the addition of secondary structure information Rfam researchers also contribute to Wikipedia's RNA WikiProject

Contents

  • 1 Uses
  • 2 Methods
  • 3 History
  • 4 Problems
  • 5 References
  • 6 External links

Uses

The Rfam database can be used for a variety of functions For each ncRNA family, the interface allows users to: view and download multiple sequence alignments; read annotation; and examine species distribution of family members There are also links provided to literature references and other RNA databases Rfam also provides links to Wikipedia so that entries can be created or edited by users

The interface at the Rfam website allows users to search ncRNAs by keyword, family name, or genome as well as to search by ncRNA sequence or EMBL accession number The database information is also available for download, installation and use using the INFERNAL software package The INFERNAL package can also be used with Rfam to annotate sequences including complete genomes for homologues to known ncRNAs

Methods

A theoretical ncRNA alignment from 6 species Secondary structure base pairs are coloured in blocks and identified in the secondary structure consensus sequence bottom line by the < and > symbols

In the database, the information of the secondary structure and the primary sequence, represented by the MSA, is combined in statistical models called profile stochastic context-free grammars SCFGs, also known as covariance models These are analogous to hidden Markov models used for protein family annotation in the Pfam database Each family in the database is represented by two multiple sequence alignments in Stockholm format and a SCFG

The first MSA is the "seed" alignment It is a hand-curated alignment that contains representative members of the ncRNA family and is annotated with structural information This seed alignment is used to create the SCFG, which is used with the Rfam software INFERNAL to identify additional family members and add them to the alignment A family-specific threshold value is chosen to avoid false positives

Performing Rfam searches using profile SCFG is very computationally expensive, and even for a small ncRNA family takes an unreasonable amount of time for a computer search To reduce the search time, an initial BLAST search is used to reduce the search space to a manageable size

The second MSA is the “full” alignment, and is created as a result of a search using the covariance model against the sequence database All detected homologs are aligned to the model, giving the automatically produced full alignment

History

Version 10 of Rfam was launched in 2003 and contained 25 ncRNA families and annotated about 50 000 ncRNA genes In 2005, version 61 was released and contained 379 families annotating over 280 000 genes In August 2012, version 110 contained 2208 RNA families, while the current version 121 annotates 2474 families

Problems

  1. Use of a BLAST search to reduce the ncRNA search space to a computationally manageable size causes reduced sensitivity in finding true homologs of the ncRNA family
  2. The genomes of higher eukaryotes contain many ncRNA-derived pseudogenes and repeats Distinguishing these non-functional copies from functional ncRNA is a formidable challenge
  3. Introns are not modeled by covariance models

References

  1. ^ a b c Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR 2003 "Rfam: an RNA family database" Nucleic Acids Res 31 1: 439–41 doi:101093/nar/gkg006 PMC 165453 PMID 12520045 
  2. ^ a b c Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A 2005 "Rfam: annotating non-coding RNAs in complete genomes" Nucleic Acids Res 33 Database issue: D121–4 doi:101093/nar/gki081 PMC 540035 PMID 15608160 
  3. ^ Gardner PP, Daub J, Tate JG, et al October 2008 "Rfam: updates to the RNA families database" Nucleic Acids Research 37 Database issue: D136 doi:101093/nar/gkn766 PMC 2686503 PMID 18953034 
  4. ^ a b Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A 2011 "Rfam: Wikipedia, clans and the "decimal" release" Nucleic Acids Res 39 Database issue: D141–5 doi:101093/nar/gkq1129 PMC 3013711 PMID 21062808 
  5. ^ "Moving to xfamorg" Xfam Blog Retrieved 3 May 2014 
  6. ^ Daub J, Gardner PP, Tate J, et al October 2008 "The RNA WikiProject: Community annotation of RNA families" RNA 14 12: 2462–4 doi:101261/rna1200508 PMC 2590952 PMID 18945806 
  7. ^ Eddy SR, Durbin R June 1994 "RNA sequence analysis using covariance models" Nucleic Acids Research 22 11: 2079–88 doi:101093/nar/22112079 PMC 308124 PMID 8029015 
  8. ^ Eddy SR 2002 "A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure" BMC Bioinformatics 3: 18 doi:101186/1471-2105-3-18 PMC 119854 PMID 12095421 
  9. ^ Nawrocki EP, Eddy SR 2013 "Infernal 11: 100-fold faster RNA homology searches" Bioinformatics 29 22: 2933–5 doi:101093/bioinformatics/btt509 PMC 3810854 PMID 24008419 

External links

  • Rfam website at the European Bioinformatics Institute
  • INFERNAL software package
  • miRBase

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