Sequence validation

We check all sequences before running a search. In order to avoid problems with the validation of your sequence, we recommend using plain, unformatted text. Here are some of the validation checks that we apply to sequences:

• sequence length must be less than 7,000 nucleotides
• the sequence must be a nucleotide sequence; protein sequences will not be accepted
• only nucleotide symbols allowed in the sequence. The accepted symbols are as A,C,G,U,T,R,Y,S,W,M,K,B,D,H, and N. Sequences containing other characters, such as "#" or "*", will not be accepted
• gap characters such as "." and "-" will not be accepted
• FASTA-header lines are accepted but will be removed

File contents

We accept only nucleotide sequences and your uploaded file must conform to a fairly strict interpretation of the FASTA file format. We apply the following checks to the format of uploaded sequence files. Files that do not conform to the following rules will be rejected by the server.

File contents

Files must contain only header lines and sequence lines. Header lines, which begin with ">", can be used to describe the sequence that follows. There is no fixed format for header lines but we restrict the characters that are allowed. If your header lines contain any of the following characters, your file will be rejected:

Note that we explicitly include the semi-colon (;) in the list of forbidden characters, although this may be used to denote comments in some versions of the FASTA-format. Please do not use comments in the FASTA files that you upload here.

Header rows

The FASTA-format specification recommends that header lines are kept shorter than 80 characters. Note that, although we do not restrict the length of header lines, the output that you will receive only shows the first 20 characters of each header line. You should therefore ensure that the sequence is identifiable using only the first twenty characters of its header.

Sequence symbols

Your sequence should be a valid nucleotide sequence. As such, the sequence line should contain only valid IUPAC nucleotide symbols, i.e. the characters A,C,G,U,T,R,Y,S,W,M,K,B,D,H,V and N, in either upper and/or lower case. In the context of a Rfam search, gaps and translation stops have little meaning and should not be used. We no longer accept gap characters such as "-" or "*".

Service limits

Searches run on a "compute farm" with a limited number of "slots". Each search takes one slot and once all slots are in use, new jobs wait in a queue for the next slot to become free. In order to prevent large jobs occupying slots for very long periods, which can impact the availability of the system for other users, we place a number of restrictions on the size of job that we will accept.

If you are planning to submit a lot of sequence searches, we recommend installing Infernal locally.

Number of sequences

Files can have up to 100 sequences.

Sequence length

Each sequence must be no longer than 7,000 nucleotides.

The search currently covers the following sections of the database:

• text fields within rfam entries, such as description and comments
• Wikipedia annotations

You can perform the same search from anywhere within the Rfam site, using the keyword search box at the top right-hand side of every page.

Species names

In order to find species names in our database, you must give the full, unabbreviated name in your query. For example, if you want to find families in Caenorhabditis elegans, you must spell out "Caenorhabditis"; "C. elegans" does not exist in the species database and will not return any results. The capitalisation of your query does not affect the results: "Caenorhabditis" is the same as "caenorhabditis".

Term suggestions

Because species names can be long, complex and easily misspelt, the form will offer suggestions for possible completions of terms that you enter. For example, as you start typing c-a-e-n, a drop-down panel will appear, showing the possible completions:

As you enter more letters, the suggestions will be refined accordingly:

Note that only the last term in the field is used to offer completions, so if you have already entered "caenorhabditis elegans", going back and shortening the first word to give "caen elegans" will not give any suggestions.

Boolean queries

Boolean queries can contain logical operators, such as AND, NOT and OR, combined with braces ("(" and ")") to form a description of a set of families with a particular species distribution.

For example, the following query:

Caenorhabditis elegans AND NOT Homo sapiens

will retrieve all families which are found in C. elegans but not in human, whilst

Caenorhabditis elegans AND Caenorhabditis briggsae AND NOT Homo sapiens

will retrieve all families which are found in both C. elegans and C. briggsae but not in human, and

( Caenorhabditis elegans OR Caenorhabditis briggsae ) AND NOT Homo sapiens

will retrieve families that are found in either C. elegans or C. briggsae but not in human.

Families unique to a single species

By checking the box marked "Find families unique to query term" you can limit the query to finding those families which are found only in a single species or taxonomic level. For example, checking the box and entering "Caenorhabditis elegans" will return a list of Rfam families that are present only in C. elegans, whilst "metazoa" will find families that exist in metazoans.

Note that you can only enter a single species term when looking for unique sequences. You will see an error message if the search field contains more than one species.

Each family in Rfam is assigned into a type category. This is based on its function. These categories are hierarchical such that something classified as a ncRNA 'gene' can be further sub-classified into a 'gene;snoRNA' which can then be further sub-classified as 'gene;snoRNA;CD-box'. A full list of the existing 'type' categories we have is provided below:

• Cis-reg
• Cis-reg; IRES
• Cis-reg; frameshift_element
• Cis-reg; leader
• Cis-reg; riboswitch
• Cis-reg; thermoregulator
• Gene
• Gene; CRISPR
• Gene; antisense
• Gene; antitoxin
• Gene; lncRNA
• 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

This search by type page allows you to browse the families by these categories. The tick boxes at each level in the tree diagram allow you to get access to the families assigned at each type level.

For example: To obtain all the families of ncRNA genes - excluding the snoRNAs- you should tick the box 'gene'. All of the boxes for the sub levels of gene will become highlighted. This would return you all families assigned to the following categories.

• gene
• gene; antisense
• gene; antitoxin
• gene; lncRNA
• gene; microRNA
• gene; ribozyme
• gene; sRNA
• gene; snRNA
• gene; snoRNA; CD-box
• gene; snoRNA; HACA-box
• gene; snoRNA; scaRNA
• gene; tRNA

To exclude all the snoRNA you can uncheck the 'snoRNA' box. This will provide you with a list of all families which are 'gene' type but not include the snoRNAs.

You should note that there are some families assigned to the 'gene' category that are not further sub classified into 'antisense', 'microRNA', 'snRNA' etc. To obtain only these families you should check the gene box and then uncheck all the sub category boxes.

Alternatively, if perhaps you are actually only interested in the snoRNAs - you can uncheck the 'gene' box and only check the 'snoRNA' box. This will return all the snoRNAs in each of the the three snoRNA sub categories (CD-box,HACA-box,scaRNA).

You can use the flexibility of this tree like structure to select for or exclude specific functional groups. The categories you are interested in do not need to be within the same branch of the tree. You can select categories from various branches such as just 'riboswitches' and 'scaRNA' to get a list of all the families that are scaRNAs or riboswitches.

The results table you obtain will list all the families in your selected categories by Rfam_accession, ID, type and description. You can then sort the results on the column data by clicking on the column headers.