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31 lines
1.3 KiB
Text
31 lines
1.3 KiB
Text
RepeatMasker is a program that screens DNA sequences for interspersed
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repeats and low complexity DNA sequences. The output of the program is a
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detailed annotation of the repeats that are present in the query
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sequence as well as a modified version of the query sequence in which
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all the annotated repeats have been masked (default: replaced by Ns).
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Currently over 56% of human genomic sequence is identified and masked by
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the program. Sequence comparisons in RepeatMasker are performed by one
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of several popular search engines including:
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- nhmmer (part of 'HMMER', available on SBo)
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- Cross_Match. Due to licensing, you should obtain this yourself:
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http://www.phrap.org
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- ABBlast/WUBlast. Due to licensing, you should obtain this yourself:
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https://blast.advbiocomp.com/licensing/
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- RMBlast (found as 'ncbi-rmblastn' on SBo)
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RepeatMasker makes use of curated libraries of repeats and currently
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supports Dfam (profile HMM library derived from Repbase sequences) and
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Repbase, a service of the Genetic Information Research Institute.
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WARNING!
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Due to the bundled databases, the installed size of this is 2.1 GB!
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NOTE!
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The package is installed in /opt. After install go fo /opt/RepeatMasker
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and run the RepeatMasker Configuration Program:
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# perl ./configure
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See README.SLACKWARE for details.
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