Rfam
See also:
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.
Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database hosted by the Wellcome Trust Sanger Institute in collaboration with Janelia Farm.[1] 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.[2] Similar to protein families, making multiple sequence alignments
(MSA) of these families can provide insight into their structure and
function. These multiple sequence alignments become more useful with
the addition of secondary structure information.
Uses of Rfam
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. [1] The database information is also available for download, installation and use using the INFERNAL software package.[3]
The INFERNAL package can also be used with Rfam to annotate sequences
(including complete genomes) for homologues to known ncRNAs.
Methods
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[1]. Each family in the database is represented by two multiple sequence alignments 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[1].
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 full alignment.
History
Version 1.0 of Rfam was launched in 2003 and contained 25 ncRNA
families and annotated about 50 000 ncRNA genes. In 2005, version 6.1
was released and contained 379 families annotating over 280 000 genes.
As of February 2007, the current version 8.1 contains 607 ncRNA
families.
Problems
- Certain ncRNA families, such as snoRNA and miRNA,
do not have conserved primary or secondary structure, and therefore
cannot be well represented in the Rfam database. However, Rfam provides
a link to miRBase, a separate miRNA database.
- 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.[2]
- Introns are not modeled by covariance models.
References
- ^ 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. PMID 12520045.
- ^ 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:10.1093/nar/gki081. PMID 15608160.
- ^ Eddy
SR (2002). "A memory-efficient dynamic programming algorithm for
optimal alignment of a sequence to an RNA secondary structure". BMC Bioinformatics 3: 18. PMID 12095421.
External links
This article is licensed under the GNU Free Documentation License. It uses material from Wikipedia Encyclopedia article "Rfam"
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