search

agshumate / Liftoff

An accurate GFF3/GTF lift over pipeline
GNU General Public License v3.0
435 stars 54 forks source link

many dots existed in amino acid sequences #113

Open shehongbing opened 2 years ago

shehongbing commented 2 years ago

Hi, First, i deeply appreciate you for the powerful tool. But, I found many dots existed in amino acid sequences when I used the liftoff. Is It mean that a pseudo-genes ?

agshumate commented 2 years ago

Hello, There could be many explanations for this, assembly errors leading to stop codons, actual variants in the genes, or the genomes are too divergent to be properly lifted over. Are you lifting over genes between assemblies of the same species?

B10inform commented 1 year ago

H agshumate,

I too have the similar problem, getting too many dots on the amino acid sequence. I have the same genome. First assembly annotation .gff3 files was used to lift the 2nd corrected assembly.

Thanks