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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