Machine learning can distinguish orphans that have resulted from sequence divergence beyond recognition.

ABSTRACT:

Motivation

Species-specific orphan genes lack homologues outside of a given taxon and frequently underlie unique species traits. Orphans can result from sequence divergence beyond recognition, when homologous proteins diverge to an extent at which sequence similarity search algorithms can no longer identify them as homologues, but they can also evolve de novo from previously noncoding sequences, in which case homologous protein-coding genes truly do not exist.

Results

Here we propose that sequence divergent orphans might be recognizable from their patterns of non-statistically significant similarity hits which are typically discarded. To test this, we simulated diverged orphan protein sequences under varying parameters. Using reversed protein sequences as negative control, w

SUBMITTER: Tassios E 

PROVIDER: S-EPMC12904771 | biostudies-literature | 2026

REPOSITORIES: biostudies-literature