rRNA prediction (hmm_rRNA)

This program predicts rRNA by using HMMER 3.0 to identify DNA reads containing rRNA sequences.
Inputs:
(1) DNA FASTA file (required)
(2) Email address (optional)
Outputs:
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):
EXAMPLE
Sequence file to upload (required): input.fasta
Email (optional): you@example.com
Show an example
Submitting......
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