Thread by @ydeigin

1/6 All right, today I got conclusive proof that Eddie Holmes sucks at aligning genomes. And if that’s not enough, I found the last nail in his “PAA insertion” coffin.

But first things first: he is a coauthor of a recent preprint with the following gem of an alignment (yellow):

2/6

See him putting the R in Rc-o319 alignment one aa ahead of others? That should immediately trigger a WTF moment in anyone even modestly familiar with genome alignments. Next, that urge should translate into checking the underlying nucleotides, which will quickly

3/6

confirm that the RSAN shouldn’t be shifted in Rc-o319 compared to its relatives but should neatly align with RSVN just above it, because it is the N in Rc-o319 that got duplicated (duplicate codons AAC AAC are a dead giveaway) — see my alignment above.

Embarrassing!!! 😂

4/6

Now, regarding that final nail in the PAA insertion coffin. Today, casually browsing through GISAID as I usually do on Friday nights, I ran into a new hot bat virus I haven’t met before: PrC31 from Yunnan.

And after checking out its alignment to my favorite RmYN02,

5/6

I couldn’t contain my excitement: the new kid on the block very nicely anchors the PAA in RmYN02 and PVA in RacCSxxx to its PIL fragment, which, in turn, aligns to SIL in ZC45/ZXC21 and others.

Translated to English, this means PAA is not a freaking insertion, Eddie!

6/6

Could someone please screenshot this for Eddie, as he had me blocked the first time I told him his PAA alignment was wrong 😂😂😂

PS: here’s his recent preprint I referred to:

biorxiv.org/content/10.110…