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Prerequisites
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- Unix system with perl 5.8.0 or higher installed
- Sequence Search Engine
RepeatMasker uses a sequence search engine to perform
it's search for repeats. Currently Cross_Match,
RMBlast and WUBlast/ABBlast are supported. You will need to obtain
one or the other of these and install them on your
system.
- For Cross_Match go to
http://www.phrap.org
You will want to select "Phred/Phrap/Consed" as
Cross_Match is part of the Phrap package.
- For RMBlast ( NCBI Blast modified for use with RepeatMasker/RepeatModeler ) please go to our download page: http://www.repeatmasker.org/RMBlast.html
- For ABBlast/WUBlast go to [ NOTE: Rights to BLAST 2.0 (WU-BLAST) have been acquired by Advanced Biocomputing, LLC. http://blast.advbiocomp.com/licensing/ The latest version of RM (3.2.8) has been modified and tested to work with ABBlast. ]
- TRF - Tandem Repeat Finder, G. Benson et al.
You can obtain a free copy at
http://tandem.bu.edu/trf/trf.html.
RepeatMasker was developed using 3.2.1.
- Repeat Database
RepeatMasker will now work with custom libraries out of the box. For
searches against standard curated species-specific repeat libraries
we highly recommend obtaining the RepeatMasker version of RepBase.
RepeatMasker searches are optimised to use this database and can
produce higher quality annotations than can be acheived using the
equivalent libraries with the -lib option.
To obtain RepBase for RepeatMasker go to
http://www.girinst.org.
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Installation
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- Download RepeatMasker
Latest Released Version: 4/26/2011: RepeatMasker-open-3-3-0.tar.gz
Previous Released Version: 7/1/2010: RepeatMasker-open-3-2-9.tar.gz
- Unpack Distribution
Unpack the distribution in your home directory or in a location where it may be shared with other users of your system ( ie. /usr/local/ ).
- cp RepeatMasker-open-3-#-#.tar.gz /usr/local
- cd /usr/local
- gunzip RepeatMasker-open-3-#-#.tar.gz
- tar xvf RepeatMasker-open-3-#-#.tar
- Install RepeatMasker Libraries
Download the libraries from http://www.girinst.org and unpack in the RepeatMasker program directory. This version
supports the following libraries ( it is always best to use the most current ): repeatmaskerlibraries-20110419.tar.gz and later.
- cp repeatmaskerlibraries-20110419.tar.gz /usr/local/RepeatMasker/
- cd /usr/local/RepeatMasker
- gunzip repeatmaskerlibraries-20110419.tar.gz
- tar xvf repeatmaskerlibraries-20110419.tar
- rm repeatmaskerlibraries-20110419.tar
- Run Configure Script
The program requires some configuration before use. There is now
a script which assists in making these changes.
- cd /usr/local/RepeatMasker
- perl ./configure
- Subscribe to announcements list
The rmannounce mailing list is an important way to hear about
bugs and new releases. This is a one-way list ( posting is not
allowed ). The traffic from the list is low and generally
mimics the major announcements shown on the main website. To subscribe
fill in the form at the bottom of this page.
RepeatMasker "open-3.0" is licensed under the Open Source License v2.1.
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Subscribing to the rmannounce Mailing List
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