Abstract
A benchmarking of the most popular orthologous identification methods using functional genomics data identifies the two best methods.
Highlights
The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics
The term describes the evolutionary relationship between homologous genes whose independent evolution reflects a speciation event, whereas paralogy refers to genes that have diverged from a common ancestor through a gene duplication event [1]
Direct conservation of functional parameters First, we measured the conservation of functional parameters between orthologous proteins, examining direct correspondence between human and mouse/worm proteins (Figures 1 and 2)
Summary
The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics. Often the definition of orthology is incorrectly interpreted as a prediction of proteins that are functionally equivalent across species, while it only defines the existence of a common ancestor for a gene in different species. The quality of the orthology prediction is an important factor in the transfer of functional annotations (and other related information). Orthology is one of the central concepts of comparative genome analysis, but is often misused as a description of functionally equivalent genes in different species. The high level of functional conservation between orthologous proteins makes orthology highly relevant for protein function prediction. At the level of protein-protein interactions, for example, it allows networks of orthologous sequences to be investigated to detect conservation of processes and pathways
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