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| author | Petar Petrov <slackalaxy@gmail.com> | 2018-01-12 22:52:20 +0000 |
|---|---|---|
| committer | Willy Sudiarto Raharjo <willysr@slackbuilds.org> | 2018-01-13 07:13:05 +0700 |
| commit | 08da4a154dfcf2a0b187b0a3a4f467eeb3b3b1e5 (patch) | |
| tree | d916bb2907a77e7f1be38d80a67729c662155408 /academic/RepeatMasker/README | |
| parent | 7e06cba42fde15af4055d31241cd224ac23ed303 (diff) | |
academic/RepeatMasker: Added (Screen DNA sequence).
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
Diffstat (limited to 'academic/RepeatMasker/README')
| -rw-r--r-- | academic/RepeatMasker/README | 31 |
1 files changed, 31 insertions, 0 deletions
diff --git a/academic/RepeatMasker/README b/academic/RepeatMasker/README new file mode 100644 index 000000000000..a62062fa85b2 --- /dev/null +++ b/academic/RepeatMasker/README @@ -0,0 +1,31 @@ +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. |