RNAmmer 1.2		INSTALLATION INSTRUCTIONS


DESCRIPTION

RNAmmer 1.2 predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA  in full genome
sequences. The method is described in detail in the following article: 

RNammer: consistent annotation of rRNA genes in genomic sequences.
Lagesen K, Hallin PF, Roedland E, Staerfeldt HH, Rognes T Ussery DW.
Nucleic Acids Res. Apr 22, 2007.

More information about the method can be found at:

	http://www.cbs.dtu.dk/services/RNAmmer/
	http://www.cbs.dtu.dk/ws/RNAmmer/

DOWNLOAD

The RNAmmer package  is a property of Center for Biological Sequence Analysis.
It may be downloaded only by special agreement.  For academic users there is a
download site at:

	http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer

Other users are requested to contact software@cbs.dtu.dk.

PRE-INSTALLATION

RNAmmer will run on the most common UNIX platforms e.g.  Linux, SunOS etc.
Make sure that your server has a complete UNIX installation. Specifically, the
following programs are necessary:

	Perl scripting language with support for Getopt::Long module installed
	hmmsearch	- the profile HMM search program from HMMER

INSTALLATION

1. Decide where you wish to keep the software. Uncompress and untar
   the package in that location:

	cat rnammer-1.2.tar.Z | gunzip | tar xvf -

   This will produce a directory  'rnammer-1.2.'.

2. Edit path specifications in the program file 'rnammer'.

3. Test RNAmmer on the test sequences shipped with the package:

	perl rnammer -S bac -m lsu,ssu,tsu -gff - < example/ecoli.fsa

4. Move or copy the 'rnammer' script to a directory in the users' path.

5. Move or copy the 'man/rnammer.1' file to a appropriate location  in your manual
   system. 

6. Enjoy ...


PROBLEMS AND QUESTIONS

In case of technical problems (bugs etc.) please contact packages@cbs.dtu.dk.

Questions on the scientific aspects of the RNAmmer method  should go to 
Peter Hallin pfh@cbs.dtu.dk.


CBS, July 19 2007