REPEATMASKER DATABASES

These are the repeat libraries for the program RepeatMasker. To
install, move or copy the files "RepeatMasker.lib" AND "version" into
the "Libraries" subdirectory of the RepeatMasker directory. 

The RepeatMasker program, maintained by Arian Smit and Robert Hubley
and copyrighted at the Institute for Systems Biology is distributed
without its repeat consensus sequence file. These sequence data are
copyrighted by the Genetic Information Research Institute and are
available at the website
http://www.girinst.org/server/RepBase/RepBase.rptmsk.tar.gz. Updates
of the databases may not always coincide with software updates Check
on this site or our server (www.repeatmasker.org) if a newer database
version is available.


INCOMPATIBILITY WITH OLDER VERSIONS OF REPEATMASKER

Whereas previous versions used multiple files with repeat consensus
sequences, RepeatMasker-open-3.1.2 of Oct 2005 and later versions use a
single EMBL file combining all types of repeats found in all different
species. The program creates a species specific set of repeat files
upon the first use of a species. This new format will be maintained
for the foreseeable future.

This (necessary) change in formatting unfortunately creates a backward
incompatibility. Older versions of the program do not work with the
new library file and vice versa. To download the last version of
RepeatMasker please visit www.repeatmasker.org



SPECIES COVERAGE

The RepeatMasker software package contains in the util directory the
script queryRepeatDatabase.pl that will print or list all repeats
included in an analysis for an indicated species. If your query
species is not covered or if you have a larger set of repeats
available, you can create your own libraries and use these with
RepeatMasker using the -lib option.


RELATONSHIP WITH REPBASE UPDATE

We're maintaining these libraries as co-editor of Repbase Update, and
are trying to keep them in synch with the RepBase Update libraries.
However, at any one time there are differences.  Entries can differ
somewhat in sequence, generally not by more than a few percent.
Reasons for this are that occasionally, independently derived
consensus sequences thrive in either database or that updates to
consensus sequences don't make it immediately to RepBase. The
nomenclature is by and large identical, but we're aware of
discrepancies and are attempting to eliminate these. One unavoidable
origin of these differences is RepeatMasker's extensive post-alignment
processing (=improvement) of the repeat annotation. To give one of
many examples, internal sequences of LTR elements can be named after
the flanking LTRs, even if there is no specific entry for that element
in the databases.

Quite a few entries in these libraries are not yet in the EMBL
formatted RepBase Update (RU) because we have not yet submitted them
formally. Others are missing from RU because it does not include all
known subfamilies. On the other hand, a few RU entries may be missing
from RepeatMasker libraries because our releases are lagging and
longer in between the RU releases (the 'version' file tells you which
is the last version of RU that is included in the current file). Also,
we do extra curation, and exclude entries in RU that give rise to
false positives, would mask genes, or do not appear to be repetitive
after all.


Arian Smit PhD
Institute for Systems Biology
Seattle, WA
asmit@systemsbiology.org

RepeatMasker software and database development and maintenance are
currently funded by an NIH/NHGRI R01 grant HG02939-01 to Arian Smit.
RepBase Update development and maintenance are funded by NIH/NLM grant
No.2P41LM006252-07A1 to Jerzy Jurka.
