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Table 1 Genome context methods implemented in this paper.

From: A systematic study of genome context methods: calibration, normalization and combination

Method (Coverage) Name Description
Phylogenetic Profiles (Full) pp-mutual-info Similarity between the phylogenetic profiles (PPs) of two genes across a list of reference genomes using the mutual information between the two PPs as similarity measure.
  pp-pearson As above, using the Pearson correlation as measure.
  pp-jaccard As above, using the Jaccard coefficient as measure.
  pp-pval As above, using the p-value of the observed PPs given by the hyper-geometric distribution that assumes that the probability of a homolog of gene G1 appearing in genome i is independent and identical to the probability of a homolog of gene G2 appearing in genome j, for all genes and all genomes.
  pp-wpval Same as pp-pval but relaxing the assumption that the probability of a homolog of a target gene appearing in genome i is the same for all i.
  pp-wpval-with-runs Similar to pp-wpval but using a heuristic to compensate for the assumption of independence of the genomes.
Gene Neighbor (Full) gn-lnX Measure of the relative distance between homologs of two genes in a list of reference genomes. The measure is given by the negative logarithm of the product of the relative distances between genes across all genomes that contain homologs for both genes.
  gn-pval P-value measure for the observed value of gn-lnX.
  gn-norm-lnX Normalized version of gn-lnX where its value is divided by the total number of genomes found to contain both homologs.
Gene Fusion (Restricted) gf P-value for the observed number of times two genes are found fused into a single gene in the reference genomes.
Gene Cluster (Restricted) gc Relative distance in bases between two genes that are adjacent and coded in the same strand in the target genome.
  1. The short name used in the rest of the paper to refer to each method is listed in the second column. The methods are explained in detail in Section 2.