Genome Property Definition Page

AccessionGenProp0152
NameDNA dinucleotide thermophily metric RR+YY-RY-YR
TypeCALCULATED
DescriptionKawashima, et al. (Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium) finds a linear relationship between optimal growth temperature (OGT) and the quantity J2, a measure of the tendency of consectutive nucleotides on one strand to both purines (RR) or both pymidines (YY). J2 is is the sum of the frequencies of consecutive purines (AA, AG, GA, GG) and consecutive pyrimidines (CC, CT, TC, TT) minus the frequencies of all other dinucleotide pairs (AC, AT, CA, CG, GC, GT, TA, TG). They report a best fit line to OGT = (293 x J2) + 46.
Parent PropertyGenProp0067: quantitative content
GenProp0067: quantitative content
GenProp0067: quantitative content
Literature References
[ 1 ]Kawashima T, Amano N, Koike H, Makino S, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto T, Nunoshiba T, Yamamoto Y, Aramaki H, Makino K, Suzuki M.  Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.  Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14257-62.  PMID 11121031
[ 1 ]Kawashima T, Amano N, Koike H, Makino S, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto T, Nunoshiba T, Yamamoto Y, Aramaki H, Makino K, Suzuki M.  Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.  Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14257-62.  PMID 11121031
[ 1 ]Kawashima T, Amano N, Koike H, Makino S, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto T, Nunoshiba T, Yamamoto Y, Aramaki H, Makino K, Suzuki M.  Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.  Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14257-62.  PMID 11121031


Parent Properties
AccessionName
GenProp0067quantitative content
GenProp0067quantitative content
GenProp0067quantitative content


Sibling Properties
AccessionName
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
GenProp0134functional gene clustering - property level
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