/***********************************************************************
#   RepeatMasker 1996-2004 by Arian Smit
#   Copyright program (C) 2000-2004  Geospiza Inc.                       
#   Copyright libraries (C) 1998-2004  Genetic Information Res. Inst.                       
#   All rights reserved.                          
#       
#   The software and databases should not be redistributed or used for
#   any commercial purpose, including commercially funded sequencing,
#   without written permission from Geospiza Inc, Seattle
#   (http://www.geospiza.com/)
/***********************************************************************

These are the repeat libraries for the program RepeatMasker. To
install, put the tar file in your RepeatMasker program directory and
untar using:
tar xzvf repeatmaskerlibraries2004March6.tar.gz

However, THE CURRENT VERSION OF THIS DATABASE IS NOT COMPATIBLE WITH
SOFTWARE RELEASED BEFORE 2004.

To get an update of the software, please follow the link to Geospiza
on the new RepeatMasker website at www.repeatmasker.org. As a new
distribution system is in place and my old administration has much
outdated information, everyone, even longtime users since 1996, will
have to fill in a new academic agreement form.


I'm maintaining these libraries as co-editor of Repbase Update, and am
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 constantly trying to eliminate these. One
unavoidable origin of these differences is RepeatMasker's extensive
post-alignment processing (improvement) of the repeat annotation. For
example, internal sequences of LTR elements can be named after the
LTRs, even if there is no specific entry for that element in the
databases (there are many more examples).

Some entries in these libraries are not yet in the reference database
of RepBase because I have not yet submitted them formally. Others are
missing, because not all subfamilies are included in that
database. RepBase Update entries may be missing from RepeatMasker
libraries because my releases are longer in between then the RepBase
Update releases (the 'version' file tells you which is the last
version of RepBase that are included in the current file). Also, I do
quite a bit of extra curating, and exclude entries that give rise to
false positives, would mask genes, or do not appear to be repetitive
after all. Finally, I am not including all species covered by RepBase,
but keep it to those species with a significant density of
interspersed repeats in their genome and for which more than just a
few repeats have been described.

For non-covered species, you can create your own libraries and use
these with RepeatMasker. Check out the fasta formatted RepBase Update
files first to see if your species has some representation there.


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