Rnammer

Introduction

From the CBS in Denmark, a tool to rind RNAs

Usage

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

man rnammer

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