rRNA prediction (hmm_rRNA)

This program predicts rRNA by using HMMER 3.0 to identify DNA reads containing rRNA sequences.
(1) DNA FASTA file (required)
(2) Email address (optional)
output.zip(including the following four files
(1) README.txt: description of the four output files
(2) output.1.coord: rRNA coordinates in original input sequence
(3) output.1.mask: input file with rRNA masked with 'N'
(4) output.1.seq: rRNA sequences in FASTA format
Usage of web server:
(1) Select the DNA fasta file in user's local computer. (required)
(2) Fill in user's email adress. (optional)
(3) Click "Submit" button. (required)
Sequence file to upload (required):
Email (optional):

you want try http://weizhongli-lab.org/metagenomic-analysis, which offers some subset of the tools.

Sequence file to upload (required): input.fasta
Email (optional): you@example.com
Show an example
Program/Database References
1."Profile hidden Markov models", S. R. Eddy Bioinformatics (1998) 14(9):755-763.
2."Identification of ribosomal RNA genes in metagenomic fragments", Y. Huang, P. Gilna and W. Li Bioinformatics (2009) 25: 1338-1340.
3. "5S Ribosomal RNA database", M. Szymanski. et al. Nucleic Acids Res. (2002) 30: 176-178.
4. "The European ribosomal RNA database", J. Wuyts et al. Nucleic Acids Res. (2004) 32: D101-D103.
Program/Database Version
Program: hmmsearch 3.0
Database: 5s Ribosomal Database (ref 3) and European rRNA database (ref 4) by 10/16/2009