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Chunk #45 — Methods — Comparative genomic analysis

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Joint mouse-human phenome-wide association to test gene function and disease risk.
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yes

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Orthologs of murine proteins from complete genomes of 77 higher eukaryotes were obtained using BLAST searches. Genomes containing paralogs of a given gene were excluded from consideration. Multiple sequence alignments of orthologs were constructed using the LINS-I algorithm in MAFFT49. Amino acid substitutions in a position corresponding to a given SNP were analysed. SNPs that occur in invariable positions in mammals were considered likely to be deleterious. Non-mammalian conservation was considered as enhancing prediction strength. SNPs that occur in variable positions in mammals were considered unlikely to be deleterious. Variable positions in rodents and primates were also considered unlikely to be deleterious.