Fig. 6
From: GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm
Case study: Local synteny adding useful information for homology inference for proteins with domain insertion. The genes CD27 in Mus musculus and TNFRSF1A in Homo sapiens are homologous and belong to the TNFR superfamily. a The domain architecture of CD27 and TNFRSF1A. CD27 has an additional Death_TNFR domain which is absent in TNFRSF1A. The NC-score (relative to the metazoan reference data) for CD27 and TNFRSF1A is 0.351, which is under the 0.5 threshold recommended for calling the genes homologous [9]. b and c Gene order conservation between Homo sapiens chr. 12, Pongo abelii chr. 12 and Mus musculus chr. 6 containing CD27 and TNFRSF1A at the center and five genes upstream and downstream in all three chromosomes. Only hits with NC-scores greater than 0.9 are displayed in these panels. Common NC-hits between CD27 gene in Mus musculus and TNFRSF1A gene in Homo sapiens are marked and used for calculating synteny correlation score between both genes. This is illustrated in (c) where CD27 in Pongo abelii is a common NC-hit of both genes. Direct synteny score between both genes (shown in b) using SyS score of GenFamClust is 0.991 and synteny correlation score between both genes using SyC score is 0.983. The GFC score obtained for this pair of genes is 0.115 which, being is greater than 0, indicates that CD27 and TNFRSF1A are homologs