Genome Property Definition Page

Namefunctional gene clustering - property level
DescriptionThe tendency of genes involved in the same process to be in the same vicinity on the DNA molecule is a measurable property of genomic organization. The metric applied here is limited to genes found in evidence of other Genome Properties whose states are "YES". An arbitrary distance of 3000 nucleotides is used to determine that genes are within a cluster. In the case on non-TIGR genomes, where both TIGR and non-TIGR gene calls are present in the CMR, whichever set gives a more complete representation of the required components is used in these calculations, defaulting to the non-TIGR gene calls in case of a tie. The value assigned for this property is the percentage of genes found in clusters compared to the total number of genes in evidence for that property. Clearly, this method will not result in fully unbiased data as each genome may contain varying numbers of YES-state properties which themselves may have varying propensities for having genes organized into clusters. In particular, a property such as CRISPR elements, which contains large clusters of genes by its very definition is problematic and has been excluded from this calculation.
Parent PropertyGenProp0067: quantitative content

Parent Properties
GenProp0067quantitative content

Sibling Properties
GenProp0003count of DNA molecules
GenProp0004count of predicted proteins
GenProp0005count of tRNAs
GenProp0020HMM hit percentage
GenProp0085DNA GC content
GenProp0086DNA size (megabases)
GenProp0108amino acid abundance (order)
GenProp0122protein average length
GenProp0152DNA dinucleotide thermophily metric RR+YY-RY-YR
GenProp0495sequenced plasmids
GenProp0799bacterial core gene set, exactly 1 per genome
GenProp0800bacterial core gene set, 1 or more per genome
GenProp0805number of ambiguous nucleotide characters
GenProp0815archaeal-only core gene set
GenProp0831archaeal core gene set, exactly 1 per genome
GenProp0832archaeal core gene set, 1 or more per genome