Searching Rfam

In addition to the quick links on the home page, every page in the Rfam site includes a Search link in the page header, which you can use to access all of the search methods that we offer:

Hint

For more details about searching Rfam, please see our paper in Current Protocols in Bioinformatics.

Text search

The Rfam text search, available on the Rfam homepage or at the top of any Rfam page, replaces the older search options, such as Keyword search, Taxonomy search, and browsing entries by type.

Using the Rfam text search one can:

• explore Rfam by category using facets

• sort results

• bookmark and share search URLs

Examples:

• families

• clans

• motifs

• families with 3D structures

• snoRNA families that match human sequences

Text search API

Text search is powered by the EBI search which supports a REST API that can be used to access the Rfam data programmatically in addition to the Rfam API.

Here is an example query that retrieves riboswitch families as well as their descriptions and the number of sequences in seed alignments:

https://www.ebi.ac.uk/ebisearch/ws/rest/rfam?query=riboswitch&format=json&fields=num_seed,description

Here is full list of fields that can be retrieved using the text search API.

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Sequence search

Searching a nucleotide sequence (DNA or RNA) against the Rfam library of covariance models will identify any regions in your sequence we would classify as belonging to one our RNA families.

Single sequence search

The Rfam sequence search is integrated with the RNAcentral sequence search so that in addition to the Rfam classification each query sequence is also searched against a comprehensive collection of ncRNA sequence from RNAcentral. The predicted secondary structure, if available, is visualised in standard orientations using R2DT.

Medium scale batch searches (less than 1,000 sequences)

If you have multiple nucleotide sequences to search, you can use our batch upload facility to upload a file of your sequences in FASTA format. Information on the format for this file can be found under the more link here. We will search your sequences against the Rfam library of covariance models and email the results back to you, usually within 48 hours. We request that you search a maximum of 1000 sequences in each file. Each sequence may be up to 200kb in length.

Large scale batch searches (more than 1,000 sequences)

If you have a large number of nucleotide searches, it may be more convenient to run Infernal searches locally (see section Genome annotation).

EBI cmscan search

The EBI cmscan service uses the same version of Infernal and the same set of Rfam covariance models as the Rfam website.

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Other ways to search Rfam

Search by entry type

Warning

Entry type search will soon be replaced by the text search.

You can search by entry type to view or download a list of families by type.

Here is a list of Rfam ncRNA types:

• Cis-reg;

  • Cis-reg; IRES;

  • Cis-reg; frameshift_element;

  • Cis-reg; leader;

  • Cis-reg; riboswitch;

  • Cis-reg; thermoregulator;

• Gene;

  • Gene; CRISPR;

  • Gene; antisense;

  • Gene; miRNA;

  • Gene; rRNA;

  • Gene; ribozyme;

  • Gene; sRNA;

  • Gene; snRNA;

  • Gene; snRNA; snoRNA; CD-box;

  • Gene; snRNA; snoRNA; HACA-box;

  • Gene; snRNA; snoRNA; scaRNA;

  • Gene; snRNA; splicing;

  • Gene; tRNA;

• Intron;

Tip

If you would like to download results as text, click Show the unformatted list at the bottom of the search results page.

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Taxonomy search

Warning

Taxonomy search search will soon be replaced by text search.

This is one of the more interesting and powerful ways to search Rfam. Using the taxonomy search form, you can identify families that are specific to a given taxonomic level or those found in a given set of taxonomic levels. You can also limit your queries to those families which are found only in a single species or taxonomic level. Please read the information under the “More…” link on the taxonomy search page for details on how to use this search.