mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-14 21:56:41 +01:00
31 lines
1.3 KiB
Text
31 lines
1.3 KiB
Text
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.
|