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Contribute to Rfam

Submit an Alignment

Contribute a Stockholm-format alignment for consideration as a new Rfam family or as an improved seed alignment for an existing family. Submissions are reviewed by our annotators and considered for the next release.

The Rfam database

Rfam is a database of non-coding RNA families. Each family is represented by a hand-curated multiple sequence alignment (the SEED), a consensus secondary structure, and a covariance model built with Infernal. The model is used to search the Rfamseq database for homologues. Rfam covers structural ncRNAs such as riboswitches, ribozymes, miRNAs, snoRNAs, rRNAs, tRNAs, and cis-regulatory elements. It is curated at EMBL-EBI and released under CC0.

Learn more about how Rfam families are built, from seed alignment curation to covariance model construction and iterative searches against Rfamseq, the underlying nucleotide sequence database of complete, non-redundant, representative genomes on which Rfam is based.

SEED sequence alignments

A SEED is a small — from few up to hundreds — hand-curated alignment of representative sequences for a family, annotated with a consensus secondary structure in WUSS notation, and we require Stockholm format. Sequences should be identified as ACCESSION/START-END, where ACCESSION is an ENA, GenBank, or RNAcentral identifier — e.g. AF228364.1/1-30 or URS0000A76344_911092/1-30.

Example:

# STOCKHOLM 1.0
#=GF ID   example_RNA
AF228364.1/1-30                CGGCAGAUGAUGAU-UUUACUUGGAUUCCC
URS0000A76344_911092/1-30      CGGCGGAUGAUGAU-UUUACUUGGGUUCCC
#=GC SS_cons                   <<<<_____________________->>>>
//

Before submitting, we recommend running our validator rfam-seed-qc. It performs checks such as sequence-length consistency, duplicates, overlapping or missing coordinates, accession validity against NCBI, SS_cons WUSS syntax, and overlap with existing Rfam families via cmscan.

Submit your alignments

Use the form below to propose a new family or improve an existing one. Provide your details, a supporting reference, the Stockholm file, and any helpful context.

Your Details

First and last name — used to follow up on your submission.

We will contact you about your submission. Your address will not be shared publicly.

Submission Type

Are you proposing a brand-new RNA family, or improving the alignment for a family already in Rfam?

Numbers only — e.g. 12345678. Look yours up at pubmed.ncbi.nlm.nih.gov.

Alignment File

Required format: Stockholm 1.0

  • First line must be exactly # STOCKHOLM 1.0
  • Last non-blank line must be exactly //
  • Accepted extensions: .sto, .stk, .stockholm, .txt
  • File size: minimum 400 bytes — maximum 5 MB
  • Plain text only (UTF-8 or ASCII) — do not upload compressed (.gz) files

Select a Stockholm-format file from your computer.

Additional Comments

Describe the RNA family, explain why this alignment is an improvement, or provide any other context that will help our annotators evaluate your submission.

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