[Biopython] Support for k-mer analyses?

Alexey Morozov alexeymorozov1991 at gmail.com
Wed Feb 8 12:41:46 UTC 2017


Hi Alan, thanks for your feedback.
You've thrown some ideas that haven't crossed my mind. I was just
wondering: why did you even find it necessary to cache distributions? What
was the scale of your work? In my experience, aminoacid distributions of
six complete eukaryotic proteomes up to k of 6 or 7 could fit into
something like seven or so gigs (with no optimisation, without even numpy),
so I thought nucleotide distributions will be prohibitive in terms of RAM
only when there are tens of them.
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