Computational protocol: Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage

Similar protocols

Protocol publication

[…] We used human coding sequence (CDS) as a probe for discontiguous Mega BLAST [] searches against the macaque whole genome shotgun trace archive (Macaca mulata WGS). For all highly similar hits in the trace archive, the full-length trace sequences were aligned using BLAT [] to the human Cernunnos-XLF gene, including introns, to ensure proper localization. The consensus sequence obtained from the alignment of individual trace sequences represents the expected macaque Cernunnos-XLF coding sequence. The predicted macaque CDS was covered by two or more sequences from the trace archive along its complete length (Fig. ). The chimpanzee Cernunnos-XLF gene was obtained from BLAT [] alignment of the human copy with the chimpanzee genome assembly, and the coding sequence homologous to human CDS was extracted. [...] Mammalian Cernunnos-XLF protein sequences were aligned using Dialign2 [] and the alignment was visualized in GeneDoc []. Synonymous and nonsynonymous substitutions were obtained using SNAP []. Gonnet PAM250 matrix [] was applied to classify substitutions as conservative or non-conservative. We considered changes to be conservative if the score was > 0.5. We used ancestral sequence reconstruction and the free ratio codon model in PAML v. 3.13 [] to reconstruct phylogeny and estimate placement of substitutions along individual branches of the phylogenetic tree. The phylogenetic tree was drawn in TREEVIEW []. [...] Structural alignment of human Cernunnos-XLF protein to the DNA repair protein XRCC4 (1fu1) was performed using 3D-PSSM [] and SWISS MODEL [] servers, analogously to ref []. The predicted structure of the human Cernunnos-XLF protein was visualized in PyMOL []. […]

Pipeline specifications

Software tools DIALIGN, PAML, TreeViewX, SWISS-MODEL, PyMOL
Applications Phylogenetics, Protein structure analysis
Organisms Homo sapiens, Pan troglodytes, Macaca mulatta, Canis lupus familiaris, Bos taurus, Giardia lamblia virus
Diseases Immunologic Deficiency Syndromes, Microcephaly