RNAhub

Load the examples:

Quick Example (this demo will not wait in the queue,execution time: ~3-5 min)
xrRNA: example of a conserved structured RNA detectable from viral genomic data

gly1RNA: example of a structured UTR detected using contextual homology in the yeast genomes (execution time: a few hours)

CWC15: example of protein coding mRNA sequence (execution time: a few hours)

U6: example of good hit to the Rfam database and the PDB, further search do not provide more information (execution time: Rfam search is instant, a full search takes a few hours)

HOTAIR: example of a conserved transcript lacking evidence for a conserved RNA structure (execution time: a few hours)

RNAhub 2.0 — experimental page

Search

Please run a maximum of 3 searches at a time, so that other users can also access the server.
The search can take up to a few hours.
There is 0 search(es) waiting in the queue right now.

E-mail address is optional

Query sequence (in the Fasta format):

Query starts and ends (should be longer than 50 nt)

Flanked sequence (containing the flanking regions and the query sequence (in the Fasta format):

Upload already-known hits/homologs. The "Query sequence" box above is not used in this mode - your sequences are used as the input alignment (input.sto), and the iterative search (v1, v2, v3) against the selected database(s) starts from it (no RepeatMasker, no Rfam scan).

Select file Change Remove

Fasta (plain hits, no alignment needed - they are aligned automatically), aligned Fasta, or Stockholm; at least two sequences.

Select genome database for your search

NCBI genome collections: Mammals - 100 genomes Vertebrate - subclustered NCBI reference vertebrate genomes Invertebrate - subclustered NCBI reference invertebrate genomes Invertebrate_60 - smaller invertebrate genome set, clustered at a lower threshold, for testing Fungi - subclustered NCBI reference fungal genomes Plants - subclustered NCBI reference plant genomes Bacteria - all NCBI reference + annotated Bacteria genomes Archaea - all NCBI genomes Virus - all available NCBI viral sequences Euglenozoa - all available NCBI genomes Other genome collections: Riboviria - NCBI RNA virus and retrovirus genomes Viral Metagenomes (IMG/VR) - metagenomic database of cultivated and uncultivated viral sequences GTDB (Genome Taxonomy Database) - 596k bacterial and archaeal genomes publicly available, both from isolated species and metagenomics INPHARED2 - curated bacteriophage genome database (41,611 genomes, Aug 2026 release, Millard Lab) INPHARED - curated bacteriophage genome database (34,076 complete genomes, Millard Lab) - not yet available in RNAhub 2.0/minidb mode, use the classic search page instead RVMT - RNA Viruses in Metatranscriptomes: ~378,000 RNA virus sequences assembled from environmental metatranscriptomes (RiboV1.4) - not yet available in RNAhub 2.0/minidb mode, use the classic search page instead

Skip RepeatMasker step

(be patient, the scan for the Rfam hits are run on the fly)