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RNAmmer 1.2 Server

The RNAmmer 1.2 server predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. This page is the entry of the CBS Prediction Server for RNAmmer. RNAmmer is available also as a Web Service described by the following WSDL file. Please read the instructions on the RNAmmer Web Services section.
This pages allows academic users to download RNAmmer

Note: Due to abuse the allowed maximum size of the submissions have been drastically lowered.

Download data

RNAmmer is run daily on the genbank sequences of the NCBI Entriez Genome Projects. MD5 checksums of the raw genome sequence are used to keep track of changes in the genome. From the links below, these data may be downloaded. Please cite Lagesen et al. 2007 when using these results

All rRNA genes fasta format rnammer-1.2.fsa.gz
GFF annotation files rnammer-1.2.gff.gz
Detailed reports from HMMsearch providing the full alignments rnammer-1.2.hmm.gz
Index of project ids, genbank accessions, organism names and sequence checksums rnammer-1.2.md5.gz

Instructions Output format Article abstract


Paste a single sequence or several sequences in FASTA format into the field below:
Select kingdom of input sequences:

Submit a file in FASTA format directly from your local disk:

At most 1,000 sequences and 1,000,000 nucleotides per submission

The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:

Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T Ussery DW RNammer: consistent annotation of rRNA genes in genomic sequences

Nucleic Acids Res. 2007 Apr 22.


Peter Fischer Hallin:        Karin Lagesen: