Rfam
Encyclopedia
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. 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 alignment
s (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.
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
. http://rfam.sanger.ac.uk
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.
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 grammar
s (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.
Database
A database is an organized collection of data for one or more purposes, usually in digital form. The data are typically organized to model relevant aspects of reality , in a way that supports processes requiring this information...
containing information about non-coding RNA
Non-coding RNA
A non-coding RNA is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA , non-messenger RNA and functional RNA . The term small RNA is often used for short bacterial ncRNAs...
(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. Rfam is designed to be similar to the Pfam
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...
database for annotating protein families.
Unlike proteins, ncRNAs often have similar secondary structure
RNA structure
Biomolecular structure is the structure of biomolecules, mainly proteins and the nucleic acids DNA and RNA. The structure of these molecules is frequently decomposed into primary structure, secondary structure, tertiary structure, and quaternary structure. The scaffold for this structure is...
without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing multiple sequence alignment
Multiple sequence alignment
A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...
s (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
Wikipedia
Wikipedia is a free, web-based, collaborative, multilingual encyclopedia project supported by the non-profit Wikimedia Foundation. Its 20 million articles have been written collaboratively by volunteers around the world. Almost all of its articles can be edited by anyone with access to the site,...
's RNA WikiProject.
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
Accession number (bioinformatics)
An accession number in bioinformatics is a unique identifier given to a DNA or protein sequence record to allow for tracking of different versions of that sequence record and the associated sequence over time in a single data repository...
. http://rfam.sanger.ac.uk
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
RNA structure
Biomolecular structure is the structure of biomolecules, mainly proteins and the nucleic acids DNA and RNA. The structure of these molecules is frequently decomposed into primary structure, secondary structure, tertiary structure, and quaternary structure. The scaffold for this structure is...
and the primary sequence, represented by the MSA
Multiple sequence alignment
A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...
, is combined in statistical models called profile stochastic context-free grammar
Stochastic context-free grammar
A stochastic context-free grammar is a context-free grammar in which each production is augmented with a probability...
s (SCFGs), also known as covariance models. These are analogous to hidden Markov models used for protein family annotation in the Pfam
Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...
database. Each family in the database is represented by two multiple sequence alignments in Stockholm format
Stockholm format
Stockholm format is a Multiple sequence alignment format used by Pfam and Rfam to disseminate protein and RNA sequence alignments. The alignment editors...
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
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
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
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
are aligned to the model, giving the automatically produced 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 January 2010, the current version 10.0 contains 1446 RNA families annotating over 3,192,596 genes.Problems
- 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.
- The genomes of higher eukaryotes contain many ncRNA-derived pseudogenes and repeats. Distinguishing these non-functional copies from functional ncRNA is a formidable challenge.
- Introns are not modeled by covariance models.