[Genome] repetitive element names

[Brooke Rhead]

Hello Nicole,

We have forwarded your question to the author of the RepeatMasker 
program.  I'll let you know what we find out.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



nicole.leahy at jax.org wrote:
> Dear USCS:
> 
> I am conducting research on repetitive elements in inbred lines of mice.  In retrieving names of repeats from the SQL server, I noticed some oddities that may or may not be mistakes.  I have been accessing:
> 
> DATABASE:  mm8
> TABLE:  chr1_rmsk
> FIELD:  repName
> 
> First, there a several pairs (and some triplets) of names where the second is the name of the first followed by "-int."  For example:
> 
> IAPLTR2_Mm
> IAPLTR2_Mm-int
> IAPLTR2_Mm-int-int
> 
> Also, there are pairs where the second name is the first followed by an underscore.  For example:
> 
> MER34C
> MER34C_
> 
> Are these distinct repeats, typos, or the result of non-standardized nomeclature?
> 
> Sincerely,
> 
> Nicole Leahy
> 
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