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)

Search

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The search can take up to a few hours.
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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):

Select genome database for your search

NCBI genome collections: Mammals - 100 genomes Vertebrate - subclustered NCBI reference vertebrate genomes Invertebrate - subclustered NCBI reference invertebrate genomes 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: Metagenomes - 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

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