PMC:5118444 / 9845-11015 JSONTXT

{"project":"2_test","denotations":[{"id":"27920798-21930507-33484679","span":{"begin":157,"end":161},"obj":"21930507"}],"text":"Analysis of selective constraint in CNV genes\nPairs of orthologous genes between Bos taurus and Homo sapiens were identified using Biomart (Guberman et al., 2011). dN/dS ratios were then computed in MATLAB (2015) using the suggested protocol. Briefly, for each ortholog pair the nucleotide sequences were translated to amino acid sequences, which were then aligned using the BLOSUM50 scoring matrix. The gaps from the aligned amino acid sequences were then copied to their corresponding nucleotide sequences, producing a codon-aligned pair of nucleotide sequences. Lastly, the synonymous (dS) and nonsynonymous (dN) substitution rates of the codon-aligned sequences were computed using the dnds function. Pairs of input sequences that were too divergent, i.e., pairs exhibiting saturation of substitutions, were removed from further analysis because a sensible dN/dS ratio could not be computed. P-values from a one-tailed Wilcoxon rank-sum test were used to test the hypothesis that dN/dS ratios of cattle genes overlapped by CNV were significantly shifted toward higher values than those of non-overlapped genes, i.e., that selection pressure is relaxed for CNV genes."}

{"project":"MyTest","denotations":[{"id":"27920798-21930507-33484679","span":{"begin":157,"end":161},"obj":"21930507"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Analysis of selective constraint in CNV genes\nPairs of orthologous genes between Bos taurus and Homo sapiens were identified using Biomart (Guberman et al., 2011). dN/dS ratios were then computed in MATLAB (2015) using the suggested protocol. Briefly, for each ortholog pair the nucleotide sequences were translated to amino acid sequences, which were then aligned using the BLOSUM50 scoring matrix. The gaps from the aligned amino acid sequences were then copied to their corresponding nucleotide sequences, producing a codon-aligned pair of nucleotide sequences. Lastly, the synonymous (dS) and nonsynonymous (dN) substitution rates of the codon-aligned sequences were computed using the dnds function. Pairs of input sequences that were too divergent, i.e., pairs exhibiting saturation of substitutions, were removed from further analysis because a sensible dN/dS ratio could not be computed. P-values from a one-tailed Wilcoxon rank-sum test were used to test the hypothesis that dN/dS ratios of cattle genes overlapped by CNV were significantly shifted toward higher values than those of non-overlapped genes, i.e., that selection pressure is relaxed for CNV genes."}