The schematic of analysis pipeline.

Abstract

<p>The orthologs of primate Chr-Y genes from the non-primate species were identified through a Basic Local Alignment Search Tool Protein-Protein (BLASTP) search against a non-primate non-redundant (nr) protein sequences database using an Expect (E)-value threshold of 10^-4 and a sequence identity greater than 35%. The genes without any possible homologs in non-primate species were considered to be primate-specific Chr-Y orphan genes. These candidates were subsequently scrutinized for any evidence of a protein-coding homolog in Chr-X or autosomes. Those genes would be excluded if there was a protein-coding gene in primate autosomes or Chr-X. The synteny comparison and sequence alignments of the candidate genes and its non-protein-coding homologs on Chr-X or autosomes would be used subsequently as the supporting information for <i>de novo</i> origin.</p