[Genome] Fwd: FW: Mouse Genome Repeat Library

[Rachel Harte]

Dear Erez,

The version of RepeatMasker and RepBase listed for mm8 is incorrect. It
should be:

RM database version 20060120
2006-01-20 (open-3-1-3) version of RepeatMasker

Sorry for the inconvenience. We will get that fixed.

Some of the repeats that you list below are in the RepeatMasker library
above:
e.g.
  ID   MER96     repeatmasker; DNA;  ???;  175 BP.
  ..
  ID   MER96B     repeatmasker; DNA;  ???;  417 BP.

  Also Mir_Mars and L3_Mars etc. but others such as ERLV-B2 and
Tigger5b are not. We contacted the authors of RepeatMasker who said that
the repeats that do not occur in the librarya are assigned by ProcessRepeats
based on the combination of alignment details and a general consensus
sequence given in the library.

In the very near future, they say that they will have an option for
RepeatMasker which will group the alignments from the RepeatMaskerLib.embl
(Repeat library file) with each of the final output lines so that the
relationship between the final output name and the original input will be
clear.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Mon, 30 Apr 2007, Erez Lieberman wrote:

> Dear UCSC Genome Browser Folks,
>
> I'm a bit puzzled about what version of the repeat masker library you are
> using for the Mm8 build of the mouse genome.
>
> In:
>
> http://hgdownload.cse.ucsc.edu/goldenPath/mm8/bigZips/
>
> It seems to say you use: RepBase Update 9.11, RM database version 20050112
>
> But you can see that there are elements like
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr1:50300388-50300718&hgsid=91559326&rmsk=full
>
> of type 'L1P5' which don't appear in that version of RepeatMasker, or in any
> other that I could find.
>
> I've found instances of the following types of elements:
>
> ['ERVL-B2', 'LTR/ERVL']
> ['MERVL-B2', 'LTR/ERVL']
> ['ERVL-D', 'LTR/ERVL']
> ['MERVL-B', 'LTR/ERVL']
> ['MERVL-C_Mm', 'LTR/ERVL']
> ['MERVL-A', 'LTR/ERVL']
> ['MERVL-_Mm', 'LTR/ERVL']
> ['L1P5', 'LINE/L1']
> ['L3_Mars', 'LINE/CR1']
> ['THER1_MD', 'SINE/MIR']
> ['MIR_Mars', 'SINE/MIR']
> ['AluG_3', 'SINE/Alu']
> ['AluF_3', 'SINE/Alu']
> ['Tigger5b', 'DNA/MER2_type']
> ['MER96B', 'DNA/hAT']
> ['MER96', 'DNA/hAT']
>
> which just don't seem consistent with the RepeatMasker databases I've seen
> at GIRI, and I've looked through all versions of repeatmasker indexed there
> (including the one mentioned above) going back past 2004.
>
> So, to sum up, what version of the repeat masker library do you use for the
> mm8 build of the mouse genome, and what version of repeatmasker do you run
> on it?
>
> Thanks!
>
> Erez Lieberman
> Broad Institute
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>