[Genome] chicken genome - missing MIRs

[Robert Kuhn]

Gyorgy,

The MIR repeats were filtered out of the list for the galGal3 assembly
at the advice of Arian Smit, author of RepeatMasker.  Here is a line from 
our assembly documentation that describes it:

    # In an email 2/13/04, Arian said we could treat all human repeats as
    # lineage-specific, but could exclude these from chicken as ancestral:
    # L3, L3a, L3b, MIR, MIR3, MIRb, MIRm

It appears, however, that chr1 somehow escaped that filtering.  

We will look into whether it is feasable to remove them from the table.
There is considerable downstream processing after the masking, however, 
and it may not make sense to remove them at this point.

best wishes,
				--b0b kuhn
				ucsc genome bioinformatics group

> From genome-bounces at soe.ucsc.edu  Wed Oct 25 09:48:34 2006
> To: <genome at soe.ucsc.edu>
> Subject: [Genome] chicken genome - missing MIRs
> 
> Dear Madame or Sir,
> 
> I recently compared the two available drafts of the chicken genome, and 
> there is a quite significant difference in the amount of MIRs in the repeat 
> annotations. In the first version there are approx 10000 MIR repeats, while 
> in the second draft 26 (!), all on the 1st chromosome. The disappearence of 
> effectively all MIRs is a bit strange, and before i proceed further I would 
> like to ask wheter there were known issues with the annotation of MIRs in 
> the first draft (2004), (or there are known issues with them in the second 
> draft [2006], i.e. SINEs were excluded from the annotations)     
> Thank you in advance.
> 
> Best wishes
> Gyorgy Abrusan
>  
> 
>  
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