Branch:
user/anddt/development/glm
11.0
12.0
12.1
12.2
13.0
13.1
13.37
14.0
14.1
14.2
15.0
bedlam
bedlam-name-fixes
dive
erik
gitignore
libressl-gopher-test
master
misc-fixes
python-renames
rworkman
urchlay
user/aclemons/updates
user/anddt/development/acpica
user/anddt/development/glm
user/anddt/development/gnustep-base
user/anddt/development/gnustep-make
user/anddt/games/assaultcube-reloaded
user/anddt/games/doomseeker
user/anddt/games/prboom-plus
user/anddt/games/rocksndiamonds
user/anddt/games/rottexpr
user/anddt/games/srb2
user/anddt/graphics/blender
user/anddt/graphics/maim
user/anddt/ham/chirp
user/anddt/ham/hamlib
user/anddt/libraries/girara
user/anddt/libraries/goffice
user/anddt/libraries/gtksourceview4
user/anddt/libraries/imlib2
user/anddt/libraries/jsoncpp
user/anddt/libraries/libnova
user/anddt/libraries/libopenmpt
user/anddt/libraries/libtorrent
user/anddt/libraries/wxGTK3
user/anddt/libraries/xmlrpc-c
user/anddt/misc/discount
user/anddt/misc/slop
user/anddt/network/nethogs
user/anddt/network/putty
user/anddt/network/rclone
user/anddt/network/rtorrent
user/anddt/network/sshguard
user/anddt/network/strongswan
user/anddt/network/umurmur
user/anddt/network/yt-dlp
user/anddt/network/znc
user/anddt/office/gnumeric
user/anddt/office/sigil
user/anddt/system/FontAwesome
user/anddt/system/conky
user/anddt/system/fakeroot
user/anddt/system/hplip-plugin
user/anddt/system/postgresql
user/anddt/system/testdisk
user/anddt/system/worker
user/anddt/system/xen
user/anddt/system/zzzfm
user/belka/updates
user/chris.willing/updates
user/dslackw/updates
user/elyk/updates
user/kingbeowulf/updates
user/mario/updates
user/ponce/updates
user/pprkut/updates
willysr
wxWidgets-wip
GPG-KEY
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Heinz Wiesinger
63daf9f79a
All: Support $PRINT_PACKAGE_NAME env var
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2 years ago | |
|---|---|---|
| .. | ||
| README | 15f3312a7e academic/RepeatMasker: Updated for version 4.1.0. | 4 years ago |
| README.SLACKWARE | 08da4a154d academic/RepeatMasker: Added (Screen DNA sequence). | 6 years ago |
| References | 08da4a154d academic/RepeatMasker: Added (Screen DNA sequence). | 6 years ago |
| RepeatMasker.SlackBuild | 63daf9f79a All: Support $PRINT_PACKAGE_NAME env var | 2 years ago |
| RepeatMasker.info | 1fd230db52 academic/RepeatMasker: update for version 4.1.2_p1 | 3 years ago |
| slack-desc | 08da4a154d academic/RepeatMasker: Added (Screen DNA sequence). | 6 years ago |
README
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 2.1 GB!
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.
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 2.1 GB!
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.