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:
- Unified text search
- Sequence search
- Other ways to search Rfam
For more details about searching Rfam, please see our paper in Current Protocols in Bioinformatics.
The new text search, available on the Rfam homepage or at the top of any Rfam page, will soon replace older search options, such as Keyword search, Taxonomy search, browsing entries by type, and Jump To navigation.
Using the new search one can:
- explore Rfam by category using facets
- sort results
- bookmark and share search URLs
The new search is a full replacement for most of the old search functionality except for taxonomy as the new search can currently find only species but not higher taxa (for example, one can search for Homo sapiens but not Mammals). Stay tuned for future updates and use the old Taxonomy search in the meantime.
Here is an example query that retrieves riboswitch families as well as their descriptions and the number of sequences in seed alignments:
Here is full list of fields that can be retrieved using the text search API.
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.
There are two ways of running sequence searches:
Both websites use the same version of Infernal and the same set of Rfam covariance models.
If your sequence is found in a genome on which rfamseq is based, your sequence will already be searched and annotated. You can paste the Genbank/EMBL accession in the text search or the “look up sequence box” on the sequence search page or a “jump to” box. The accession version number is not required.
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.
If you have a large number of nucleotide searches, it may be more convenient to run Infernal searches locally (see section Genome annotation).
The old keyword search will soon be replaced by the Unified text search.
Each page in the Rfam site contains a keyword search box in the header. This is the broadest text search we offer and you can use this to find all Rfam families that match a particular keyword. The search will try to match your query term against textual information from several different sections of the Rfam database:
- text fields for Rfam families, such as family descriptions and identifiers
- Rfam associated Wikipedia entries
- literature reference titles and authors
- PDB structures
Your keyword should be a simple text string (letters and numbers), but underscores, hyphens, periods and spaces are also accepted. Wildcard terms are not necessary, since the search system will add wildcards to the end of your search terms. If in doubt, use the shortest text string you can and you will receive the widest set of possible matches. You can then sort the results and refine your search if needed.
Do remember that the keyword search tries to match against all of the sections of the database, including the Wikipedia article, so if your term is mentioned in the family description text, you will also get a match.
If you search with two terms at once your will only receive a result if a match is found for both terms.
Search results page
Your query term is reported and, if the term you used exactly matched a family ID or accession, this is also reported. This text is followed by a small table that provides a summary showing in which section of the database your query string was found.
The larger table that follows provides links to the families that have a match to your query in at least one section of the database. Each matching family is listed only once, though it may have matches in more than one section of the database. For each family with a match we report:
- accession (linked to the the family page)
- identifier (linked to the family page)
- family description line
- between one and four columns that specify in which of the sections of the database the match was found
If your query term does not match any data in the database, you will be taken to a ‘no results’ page which will offer you tips on how to refine your search.
Entry type search will soon be replaced by the Unified 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; IRES;
- Cis-reg; frameshift_element;
- Cis-reg; leader;
- Cis-reg; riboswitch;
- Cis-reg; thermoregulator;
- 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;
If you would like to download results as text, click Show the unformatted list at the bottom of the search results page.
Taxonomy seach search will soon be replaced by the Unified 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.
The Browse link at the top of each page will take you to an index page, from which you can browse all Rfam families by their family names (otherwise known as the Rfam IDs). These are the familiar names for the RNA, such as “tRNA” or “Hammerhead_1”. The families are organised alphabetically and you can use the ranges (A-F, G-L etc) to take you to the appropriate place in the list. Families where the name begins with a number (e.g. “6S”, “7SK”) can be found under the 0-9 index.
“Jump to” search will soon be replaced by the Unified text search.
Many pages in the site include a small search box, entitled “Jump to…”. The “Jump to…” box allows you to go immediately to the page for any entry in the Rfam site. This is primarily useful when you know the family or the sequence accession you are interested in.
The “Jump to…” search understands Genbank/EMBL accessions, Rfam family accessions and identifiers for most types of entry. For example, to find a particular family, you can enter either an Rfam family accession, e.g. RF00198, or, if you find it easier to remember, a family ID, such as SL1. This will take you to the main entry for this family. Note that the search is case insensitive. Searches for family identifiers such as ‘RNase’ or ‘mrp’ will be too ambiguous and you will get an error “Couldn’t guess entry”. In this case you need to specify the the full family name, e.g. RNase_mrp’. If you want to search with an ambiguous family identifier use the keyword search instead.
Alternatively, if you are interested in the annotations to a particular sequence or genome you can use the Genbank/EMBL accession, e.g. AE017225 and you will be taken to a list of the relevant Rfam family annotations to this sequence. This also works for EMBL CON files, e.g. CM000428.
The order in which the search tries to match your query term against the various types of ID and accession in the database is:
- Rfam accession, e.g. RF00198
- Rfam identifier, e.g. SL1
- Genome Genbank/EMBL accession, e.g. AE017225
- Sequence Genbank/EMBL accession e.g. AF325543
If all of the guesses fail, you’ll see an error message saying “Entry not found”.