[Fwd: EMBOSS:einverted and "nested" inverted repeats]

[Gary Williams, Tel 01223 494522]

Linda Cardle (lcardl at scri.sari.ac.uk) wrote:
> 
> I wasn't sure who to contact about this query, but here goes:
> 
> I'm trying to find MITES within sequences using einverted. My main question
> is:
> 
> How does einverted cope with "nested" inverted repeats?
> 
> My reason for asking is that to simulate a sequence with both an inverted
> repeat and an SSR inverted repeat I added an SSR inverted repeat inside a
> known MITE. Once I'd done that it seemed that einverted could spot the SSR
> but not the MITE surrounding it.
> 
> I was hoping you'd be able to clarify how einverted would cope with this
> situation, or point me to someone who could.
> 
> Thanks for your time,
> Linda
> --
> Dr Linda Cardle
> Computational Biology
> Scottish Crop Research Institute
> Dundee, DD2 5DA

-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK