Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins
Fig 2
Performance of graph alignment.
The mean fraction of true-positive pairings (TP fraction) is shown as a function of the number k of nearest neighbors in the kNN graph for 100 GA realizations (blue). Performance for the orthology graph is also shown (red)—but note that it does not depend on k. Error bars (shaded regions) correspond to one standard deviation. The mean TP value of the IPA starting without any training set of known paired sequences is shown for comparison (yellow). It was obtained using Nincrement = 6 and by averaging over 50 replicates that differ in their initial random pairings, cf. Materials and methods. The dotted black line shows the average TP fraction obtained for random HK-RR pairings within species (null model).