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Explanation of the "Details Page"

PHRINGE ID numbers have been assigned arbitrarily to each gene model from each genome. These numbers are assigned to each genome as follows:

  Genome
From gene number
To gene number
  Hyaloperonospora arabidopsidis
1
15,512
  Phytophthora infestans
15,513
38,171
  Phytophthora ramorum
38,172
53,915
  Phytophthora sojae
53,916
72,943
  Phaeodactylum tricornutum
72,944
82,969
  Pythium ultimum
82,970
98,292
  Thalassiosira pseudonana
98,293
109,682


VMD is the “Virginia Microbial Database”, which hosts detailed information on the genes of P. sojae, P. ramorum, and H. arabidopsidis. (The latter is synonymous with the older names Hyaloperonospora parasitica and Peronospora parasitica.) VMD has also assigned arbitrary gene IDs to each gene model which can be entered here to call up this page for the corresponding gene.

The third box on this page contains genes from all included genomes that have a distance score from a pairwise global alignment below the specified "maximum distance to show". The "maximum number of matches" per taxon to show can also limited. The "maximum distance to show" defaults either to the score of the seed of the cluster for this gene or to zero, which in this case means that no limit is specified (in contrast to it’s normal meaning of sequence identity).

The length and difference in length are both numbers of amino acids for the proteins.

In the bottom box, the Cluster IDs link to the corresponding Cluster and Compare Page. The cluster type refers to the specific node on the tree where a cluster was built that includes this gene.