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14.2 > Academic > RepeatMasker (4.0.7)

RepeatMasker 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 (default: replaced by Ns).

Currently over 56% of human genomic sequence is identified and masked by
the program. Sequence comparisons in RepeatMasker are performed by one
of several popular search engines including:

- nhmmer (part of 'HMMER', available on SBo)
- Cross_Match. Due to licensing, you should obtain this yourself:
http://www.phrap.org
- ABBlast/WUBlast. Due to licensing, you should obtain this yourself:
https://blast.advbiocomp.com/licensing/
- RMBlast (found as 'ncbi-rmblastn' on SBo)

RepeatMasker makes use of curated libraries of repeats and currently
supports Dfam (profile HMM library derived from Repbase sequences) and
Repbase, a service of the Genetic Information Research Institute.

WARNING!
Due to the bundled databases, the installed size of this is 1.8 GiB!

NOTE!
The package is installed in /opt. After install go fo /opt/RepeatMasker
and run the RepeatMasker Configuration Program:

# perl ./configure

See README.SLACKWARE for details.

This requires: ncbi-rmblastn, perl-Text-Soundex, trfind, HMMER

Maintained by: Petar Petrov
Keywords: screen,dna,sequence,repeat,interspersed repeats,mask,low complexity
ChangeLog: RepeatMasker

Homepage:
http://www.repeatmasker.org/

Source Downloads:
RepeatMasker-open-4-0-7.tar.gz (4dcbd7c88c5343e02d819f4b3e6527c6)

Download SlackBuild:
RepeatMasker.tar.gz
RepeatMasker.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Validated for Slackware 14.2

See our HOWTO for instructions on how to use the contents of this repository.

Access to the repository is available via:
ftp git cgit http rsync

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