RepeatMasker 4.0.3

RepeatMaskerRepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (i.e. replaced by Ns or put to lowercase). RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).

Module file

The module file can be found in this location:

 /cm/shared/apps/WUR/ABGC/modulefiles

<source lang='tcl'>

1. %Module1.0#######################################################################
   1. RepeatMasker 4.0.3 modulefile

proc ModulesHelp { } {

       puts stderr "\tAdds RepeatMasker v4.0.3 to your environment"

}

module-whatis "Adds RepeatMasker v4.0.3 to your environment"

set repeatmasker_403_root /cm/shared/apps/WUR/ABGC/RepeatMasker/RepeatMasker-4-0-3/

prepend-path PATH $repeatmasker_403_root

</source> Please note that Maker requires the system tempdir to be in a non-NFS location. To be safe, best to put it in a local disc. For that reason the TMPDIR environment variable gets set to /local. Also note that Maker requires an Sqlite database. Sqlite databases are (currently) not compatible with the Lustre file system.

Installation details

Pre-compiled rmblast (NCBI BLAST+ optimized for RepeatMasker) downloaded from the RepeatMasker download pages. Location of rmblast:

 /cm/shared/apps/WUR/ABGC/blast/rmblast-2.2.28

The default search engine is 'ncbi' (rmblast). Alternative search engines are possible. Currently, only hmmer 3.1 is installed as alternative search engine.

Pre-compile binary of Tandem Repeat Finder (TRF,trf) v4.0.4 were downloaded from the TRF homepage and can be found:

 /cm/shared/apps/WUR/ABGC/tandem_repeat_finder/trf404.linux64

The soft links 'TRF' and 'trf' can be found in the same folder. Some programs (e.g. RepeatModeler) may require this as default binary name.

Installed RepBase libraries include the 2013-04-22 RepeatMasker version. Dfam 1.2 is provided as default in the RepeatMasker package.

 /cm/shared/apps/WUR/ABGC/RepeatMasker/RepeatMasker-4-0-3/Libraries

See also

• Globally installed software
• ABGC specific modules

External links

• RepeatMasker homepage
• RepBase homepage