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. |