[EMBOSS] how string is shuffleseq

[Daniel Barker]

Dear Derek,

Not a direct answer to your question - but there was an interesting 
paper on shuffling recently, did you see it:

Jiang et al. (2008) uShuffle: A useful tool for shuffling biological 
sequences while preserving the k-let counts. BMC Bioinformatics 9: 192.

Best wishes,

Daniel

Derek Gatherer wrote:
> Dear EMBOSS experts
> 
> How good a shuffler is shuffleseq?  I have always believed that it 
> shuffles beyond all recognition, since tracer words inserted into a 
> database are always gone after 1 round of shuffling.  But are there any 
> hard test data on its shuffling strength?  For instance, for any, say, 
> 100-mer, what fragments would reasonably be expected to remain after 
> shuffling?  Should I be surprised to see a 15-mer from the 100-mer still 
> intact??
> 
> Sorry I can't express this more precisely.  I thinks it's probably 
> clear...  I ask as there is a piece of software I am testing on real 
> genomes and their shuffled derivatives, and I want to exclude the 
> possibility that the control is compromised by an inadequacy of shuffling.
> 
> Cheers
> Derek
> 
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-- 
Daniel Barker
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