[DAS] DAS and bacterial genomes
biopython at maubp.freeserve.co.uk
Wed Aug 18 11:23:56 UTC 2010
On Wed, Aug 18, 2010 at 11:02 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> Just to say that I think we should get this as straight as we can; just to
>> state the obvious - EG is not trying to be deliberately complex here, it is
>> just that the concept of "one taxid == one species == one assembly series" just
>> breaks down in bacteria.
> Could it be treated as "one taxid == one strain == one assembly"?
I'm sticking my oar in here, and probably this is obvious, but anyway...
Surely it has to be "one taxid == one strain == multiple assemblies"? And this
isn't just for Bacteria, but all organisms. After all, "the" human sequence
has already gone through several revisions (hg18 and hg19 being the latest).
Even things like the E coli K12 sequence have gone through multiple revisions
What about multiple individual genomes from the same taxid? What I am
thinking of here is different human genomes - do we call Craig Ventor a
strain of human with his own taxid? That doesn't seem like it will scale well ;)
Would we have an extra level here,
i.e. one taxid == one strain == multiple individuals,
one individual == multiple assemblies
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