 | |
| Content | |
|---|---|
| Description | The Rfam database provides alignments, consensus secondary structures and covariance models for RNA families. |
| Data types captured | RNA families |
| Organisms | all |
| Contact | |
| Research center | EBI |
| Primary citation | PMID 33211869 |
| Access | |
| Data format | Stockholm format |
| Website | rfam |
| Download URL | FTP |
| Miscellaneous | |
| License | Public domain |
| Bookmarkable entities | yes |
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,[1][2][3][4] and currently hosted at the European Bioinformatics Institute.[5] 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.[4][6]
- ^ 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:10.1093/nar/gkg006. PMC 165453. PMID 12520045.
- ^ 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:10.1093/nar/gki081. PMC 540035. PMID 15608160.
- ^ Gardner PP, Daub J, Tate JG, et al. (October 2008). "Rfam: updates to the RNA families database". Nucleic Acids Research. 37 (Database issue): D136–D140. doi:10.1093/nar/gkn766. PMC 2686503. PMID 18953034.
- ^ 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:10.1093/nar/gkq1129. PMC 3013711. PMID 21062808.
- ^ "Moving to xfam.org". Xfam Blog. Retrieved 3 May 2014.
- ^ Cite error: The named reference
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