Microbes of all sorts, mainly aquatic, but open to all biomes. That is what I use my bioinformatics for. Also posting baby stuff now apparently, for some reaso
Uppsala, Sverige
Joined May 2016
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Moritz Buck retweeted
Apply to this long-term #postdoc position!
Come and join us in our marvelous path towards understanding the role of phage co-infection in their genome evolution and become a member of the *MULTIPHAGE* #ERCStG team!
Please retweet or is it reX now😉
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Combinatorial sequence analysis: try the forward, then the reverse, and the rev-comp, and then repeat with R2, pick whatever matches most....
Nah, dumber, the static layout is just based on a graph where the edges connect all genomes that have an ANI > 91.5 (slightly arbitrary, to have a reasonable picture)
Well, I can't get convinced by the recombination barrier until we find a species that doesn't recombine... Anyhow, the same threshold doesn't work for some pelagi' species (they still have a barrier though) which lead me to this rabbit hole...
There is no real dimensionality reduction, it's just a standard fruchterman-reingold graph layout ^^
Well then i would hope the second file starts with a new entry and at least I'd see a "greater than" lost in the middle of it... Uhhh all the dirty scenarios i have in my mind now....
All smoke mirrors and more, won't doesn't matter if on 3 years postdoc you have 5 contracts, got asked to quit because the money moved faculty and told after 2.5 years grant hasn't enough money because you're not allowed to consider obligatory salary increases... #BitterPostDoc
I replied anyhow, but i know the story it comes out of and i think it's easy to misconstrue some aspects of this discussion without enough context.....
I do have to complain, the whole first page of questions already assumes i accept data embargoes.... Makes it difficult for me to answer without making it look like i stand behind that practice... Also, it's very black and white...
All of that. But if NCBI not there the NCBI taxonomy interface of biopython can do the job, or taxize for R.
The restful API is weirdly useable, between the KO entries and the ORG entries can get some info there, and can be done with `wget` and bash. But wouldn't trust it to much... It would be buased on validated stuff. I would probably run kofamscan against nr or something