Michael Hiller

You mean finding the branch in the phylogenetic tree where the gene originated? E.g. finding a gene conserved between human and rodents/lagomorphs but not outside Euarchontoglires, one can infer that...

60 My between nematodes will be like human-mouse in molecular distance. A better metric would be ~0.6 or less subs per neutral sites in the genome.

Can you pls extract only projections (transcript.gene.chainID) that are classified as intact or partially intact? This info is in loss_summ_data.tsv.gz (https://genome.senckenberg.de/download/TOGA/README.txt). Other projections have frameshifts or stop codons or missing...

Can you send an example? We have all the data also in the genome browser http://genome.senckenberg.de/ Pls type a projection into the browser of the query species and click on...

For which assembly are these stats? And how does that compare to the BUSCO stats we have in the supplement tables?

This is the HLdinBra1 DNAzoo assembly, right? Of course, mouse or human as the reference will make a difference, but can't explain 97.8% vs. 76% completeness. Can you pls download...

Likely TOGA masks frameshifts and internal stop codons, while your GTF to protein may not do that. This could explain it. Can you look at BUSCO genes that are complete...

20000 genes are 1:0. This is the main problem. Can you visualize your chains in the UCSC browser? E.g. convert to bigChain and load as a custom track? How large...

Can you pls point me to the query assembly you used? I can try to produce the chains here. Then you can compare it.

Thx. Is the query actually available on NCBI or DNAzoo ? Or is this a private assembly? Is hg38 your reference?