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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