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Fig. 7 | BMC Evolutionary Biology

Fig. 7

From: GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm

Fig. 7

Case study: Local synteny adding useful information for homology inference for highly divergent proteins. The genes Usp26 in Mus musculus and USP46 in Homo sapiens are homologous and belong to the USP superfamily. Both proteins are single domain proteins belonging to the Peptidase_C19 superfamily. The NC-score (relative to the metazoan reference data) for USP46 and Usp26 is 0.411, which is under the 0.5 threshold recommended for calling the genes homologous [9]. a and b Gene order conservation between Homo sapiens chr. 4, Homo sapiens chr. X and Mus musculus chr. X containing Usp26 and USP46 at the center and five genes upstream and downstream in all three chromosomes. Only hits with NC-scores greater than 0.7 are displayed in these panels. Common NC-hits between Usp26 gene in Mus musculus and USP46 gene in Homo sapiens are marked and used for calculating synteny correlation score between both genes. This is illustrated in (b) where USP26 in Homo sapiens is a common NC-hit of both genes. Direct synteny score between both genes (shown in a) using SyS score of GenFamClust is 0.741 and synteny correlation score between both genes using SyC score is 0.672. The GFC positive score obtained for this pair of genes, 0.045, indicates that Usp26 and USP46 are homologs despite high sequence divergence and little sequence similarity

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