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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:
- ABBlast/WUBlast. Due to licensing, you should obtain this yourself:
- 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.
Due to the bundled databases, the installed size of this is 2.1 GB!
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.