Rnammer - Revision history

Rf at 15:11, 10 August 2016

2016-08-10T15:11:28Z

Rf at 15:11, 10 August 2016

2016-08-10T15:11:02Z

Rf at 15:10, 10 August 2016

2016-08-10T15:10:06Z

Rf: Created page with "= 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 p..."

2016-08-10T15:07:33Z

Created page with "= 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 p..."

New page

= 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

@@ Line 87: / Line 87: @@
    EXAMPLE
          core-rnammer configuration.cf
-−
   AUTHORS
          Peter Fischer Hallin (pfh@cbs.dtu.dk) Center  for  Biological  Sequence

← Older revision		Revision as of 15:11, 10 August 2016
Line 87:		Line 87:
	EXAMPLE		EXAMPLE
	core-rnammer configuration.cf		core-rnammer configuration.cf
		+
		+	AUTHORS
		+	Peter Fischer Hallin (pfh@cbs.dtu.dk) 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)

@@ Line 14: / Line 14: @@
 It's given here:
   RNAmmer(1)							    RNAmmer(1)
   NAME
@@ Line 31: / Line 28: @@
          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
+         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,
@@ Line 58: / Line 52: @@
          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
@@ Line 65: / Line 58: @@
          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
-        -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