From the CBS in Denmark, a tool to rind RNAs
To load the module
module load rnammer
This module will already be loaded if you have loaded the prokka module.
This tool does not really have a helpfile, however, it does have manual page, obtained by typing
It's given here:
RNAmmer(1) RNAmmer(1) NAME RNAmmer - predicts ribosomal RNA genes in prokaryotic genome sequences SYNOPSIS rnammer [-S kingdom] [-m molecules] [-xml xml-file] [-gff gff-file] [-d] [-p] [-h hmmreport] [-f fasta-file] [sequence] or rnammer [-S kingdom] [-m molecules] [-xml xml-file] [-gff gff-file] [-d] [-p] [-h hmmreport] [-f fasta-file] < [sequence] CORE core-rnammer [configuration] DESCRIPTION RNAmmer predicts ribosomal RNA genes in full genome sequences by util- ising two levels of Hidden Markov Models: An initial spotter model searches both strands. The spotter model is constructed from highly conserved loci within a structural alignment of known rRNA sequences. Once the spotter model detects an approximate position of a gene, flanking regions are extracted and parsed to the full model which matches the entire gene. By enabling a two-level approach it is avoided to run a full model through an entire genome sequence allowing faster predictions. RNAmmer consists of two components: A core Perl program, ’core-rnam- mer’, and a wrapper, ’rnammer’. The wrapper sets up the search by writ- ing on or more temporary configuration(s). The wrapper requires the super kingdom of the input sequence (bacterial, archaeal, or eukary- otic) and the molecule type (5/8, 16/17s, and 23/28s) to search for. When the configuration files are written, they are parsed in parallel to individual instances of the core program. Each instance of the core program will in parallel search both strands, so a maximum of 3x2 hmm- search processes will run simultanously. The input sequences are read from sequence or. The input must be in Pearson FASTA format. When using the core program, input configuration must in RNAmmer configuration file format (see documentation below) The output is controlled by options h (hmmreport), and f (fasta). REQUIREMENTS The main executable ’rnammer’ requires the core RNAmmer program ’core- rnammer’. The core program requires the binary ’hmmsearch’ (http://hmmer.wustl.edu/) OPTIONS -S Specifies the super kingdom of the input sequence. Can be either ’arc’, ’bac’, or ’euk’. -gff output gff file Specifies filename for output in GFF version 2 output -multi Runs all molecules and both strands in parallel -f fasta Specifies filename for output fasta file of predicted rRNA genes -h hmmreport Specifies filename for output HMM report. -m Molecule type can be ’tsu’ for 5/8s rRNA, ’ssu’ for 16/18s rRNA, ’lsu’ for 23/28s rRNA or any combination seperated by comma. [sequence] The input file to process. EXAMPLE core-rnammer configuration.cf AUTHORS Peter Fischer Hallin (firstname.lastname@example.org) Center for Biological Sequence Analysis (CBS) Technical University of Denmark February 2006 REFERENCES RNAmmer: consistent annotation of rRNA genes in genomic sequences Lage- sen K, Hallin PF, Rodland EA, Staerfeldt HH, Rognes T, and Ussery DW. Manuscript in preparation Information and web-service can be found at the internet address: http://www.cbs.dtu.dk/services/RNAmmer/ SEE ALSO fasta(1), hmmsearch(1)