POCP X AAI

[shlomobl]

Hi,

How does POCP compare to Average Amino acid Identity (AAI)?

Both calculation wise and interpretative/biologically speaking.

[hoelzer]

Hey,

You might want to check the original POCP publication: https://journals.asm.org/doi/10.1128/jb.01688-14

Unfortunately, they mainly compare POCP to ANI and 16S rRNA gene identity (see also Supplement).

Regarding the calculation, the difference is:

AAI: Measures the average sequence similarity of all orthologous protein sequences shared between two genomes

• Identify all orthologous protein-coding genes between two genomes
• Computes the amino acid sequence identity for each ortholog pair (pairwise alignment)
• Averages the identity values of all ortholog pairs

Interpretation: AAI (%) across shared genes

POCP: Estimates the percentage of conserved proteins between two genomes.

• Identify all proteins in genome A that have homologs in genome B and vice versa
• Calculate the fraction of proteins in one genome that have homologs in the other genome
• Use specific thresholds (e.g., 40% identity and 50% coverage) to determine homology, thus not all proteins will make it into the comparison

Interpretation: Percentage of total proteins in each genome that are conserved