1/2) #bioinformatics people interested in #genome alignment, has anyone tried to do "adaptive seeding throttling" where after a long run time a lastz job would go into an adaptive mode where it detects that a specific repeat is initiating too many seeds, which would trigger lastz to mask it?
It is unfortunate that this has to be reminded so much to reviewers at all steps: doing this things right or at least as well as possible IS in itself a strong innovation.
You know you have great collaborators when they bring your own enthusiasm back at times when it has been vacillating. You know who you are :).
A bad case of using a non official gene/protein name that makes it even worse by introducing ambiguity with another gene name. This makes curation efforts far more difficult:
pmc.ncbi.nlm.nih.gov/articles/PMC...
2/2) lastz requires to pre-softmask the genomes extensively which is itself very computationally costly, and since it is often a handful of problematic jobs, it seems more efficient to have lastz mask problematic repeats itself? @hillermich.bsky.social have you though about improving lastz?
I have been told that in reference to the big confs in my field, the smaller ones are always very inclusive. Having observed social dynamics at those big confs I see where they come from.
Some deep work by my former student Matthew Aguirre on what the properties of cis- and trans eQTLs can teach us about the structure of gene regulatory networks!
Ils ont entouré le cadre prévu?
Your work is very inspiring, a lot to do around compensatory evolution. For us it indirectly reveals virus-driven adaptation, with the big advantage of being hopefully able to do it just with divergence. Viruses seem very good at forcing changes where they usually do not happen due to constraint.
Deeply interesting comment on a paper on compensatory evolution following "host" adaptation to a selfish genetic element. Reminescent of our finding of compensatory protein stability evolution after ancient viral epidemics. #evolution www.nature.com/articles/s41...