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Volumn 34, Issue 4, 2008, Pages 661-668

Codon evolution is governed by linear formulas

Author keywords

Amino acid composition; Codon evolution; Codon usage; Genome; Linear empirical formula; Nucleotide content

Indexed keywords

NUCLEOTIDE; SINGLE STRANDED DNA;

EID: 43149124638     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-007-0024-3     Document Type: Article
Times cited : (12)

References (42)
  • 1
    • 33845214633 scopus 로고    scopus 로고
    • Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transcriptions
    • Albrecht-Beuhler G (2006) Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transcriptions. Proc Natl Acad Sci USA 103:7828-17833
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 7828-17833
    • Albrecht-Beuhler, G.1
  • 2
  • 3
    • 0033531431 scopus 로고    scopus 로고
    • Deviations from Chargaff's second parity rule correlate with direction of transcription
    • Bell SJ, Forsdyke R (2006) Deviations from Chargaff's second parity rule correlate with direction of transcription. J Theor Biol 197:63-76
    • (2006) J Theor Biol , vol.197 , pp. 63-76
    • Bell, S.J.1    Forsdyke, R.2
  • 4
    • 0000897884 scopus 로고
    • Chemical specificity of nucleic acids and mechanism of their enzymatic degradation
    • Chargaff E (1950) Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia VI:201-209
    • (1950) Experientia , vol.6 , pp. 201-209
    • Chargaff, E.1
  • 5
    • 0027219970 scopus 로고
    • A vectorized sequence-coupling model for predicting HIV protease cleaveage sites in proteins
    • Chou K-C (1993) A vectorized sequence-coupling model for predicting HIV protease cleaveage sites in proteins. J Biol Chem 268:16938-16948
    • (1993) J Biol Chem , vol.268 , pp. 16938-16948
    • Chou, K.-C.1
  • 6
    • 0032940342 scopus 로고    scopus 로고
    • Protein subcellular location prediction
    • Chou KC, Elrod DW (1999) Protein subcellular location prediction. Protein Eng 12:107-118
    • (1999) Protein Eng , vol.12 , pp. 107-118
    • Chou, K.C.1    Elrod, D.W.2
  • 7
    • 0027054450 scopus 로고
    • Diagrammatization of codon usage in 339 HIV proteins and its biological implication
    • Chou KC, Zhang CT (1992) Diagrammatization of codon usage in 339 HIV proteins and its biological implication. AIDS Res Hum Retroviruses 8:1967-1976
    • (1992) AIDS Res Hum Retroviruses , vol.8 , pp. 1967-1976
    • Chou, K.C.1    Zhang, C.T.2
  • 9
    • 0009746985 scopus 로고
    • Building a phylogenetic trees: Cytochrome C
    • National Biomedical Fundation, Washington, D.C.
    • Dayhoff MO, ParkCM, McLaughlin PJ (1977) Building a phylogenetic trees: cytochrome C. In Atlas of protein sequence and structure. Vol. 5, National Biomedical Fundation, Washington, D.C., pp 7-16
    • (1977) Atlas of Protein Sequence and Structure , vol.5 , pp. 7-16
    • Dayhoff, M.O.1    Parkcm2    McLaughlin, P.J.3
  • 11
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124-2128
    • (1999) Science , vol.284 , pp. 2124-2128
    • Doolittle, W.F.1
  • 12
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
    • (2001) Nature , vol.409 , pp. 860-921
  • 13
    • 0031593216 scopus 로고    scopus 로고
    • Influence of genomic G + C content on average amino-acid composition of proteins from 59 bacterial species
    • Lobry JR (1997) Influence of genomic G + C content on average amino-acid composition of proteins from 59 bacterial species. Gene 205:309-316
    • (1997) Gene , vol.205 , pp. 309-316
    • Lobry, J.R.1
  • 14
    • 0037179524 scopus 로고    scopus 로고
    • Asymmetric directional mutation pressures in bacteria
    • research0058.1-0058.14
    • Lobry JR, Sueoka N (2002) Asymmetric directional mutation pressures in bacteria. Genome Biol. 3: research0058.1-0058.14
    • (2002) Genome Biol , vol.3
    • Lobry, J.R.1    Sueoka, N.2
  • 15
    • 0028338701 scopus 로고
    • Phylogeny from function: Evidence from the molecular fossil record that tRNA originated in replication, not translation
    • Maizels N, Weiner M (1994) Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci USA 91:6729-6734
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 6729-6734
    • Maizels, N.1    Weiner, M.2
  • 16
    • 0032169578 scopus 로고    scopus 로고
    • Replicational and transcriptional selection on codon usage in Borrelia burgdorferi
    • McInerney JO (1998) Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA 95:10698-10703
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 10698-10703
    • McInerney, J.O.1
  • 18
    • 33749149265 scopus 로고    scopus 로고
    • Deviations from Chargaff's second parity rule in organelle DNA insights into the evolution of organelle genomes
    • Nikolaou C, Almirantis Y (2006) Deviations from Chargaff's second parity rule in organelle DNA insights into the evolution of organelle genomes. Gene 381:34-41
    • (2006) Gene , vol.381 , pp. 34-41
    • Nikolaou, C.1    Almirantis, Y.2
  • 19
    • 0027305701 scopus 로고
    • Symmetry observations in long nucleotide sequences
    • Prabhu VV (1993) Symmetry observations in long nucleotide sequences. Nucleic Acids Res 21:2797-2800
    • (1993) Nucleic Acids Res , vol.21 , pp. 2797-2800
    • Prabhu, V.V.1
  • 20
    • 0034949341 scopus 로고    scopus 로고
    • Compositional symmetries in complete genomes
    • Qi D, Cuticchia J (2001) Compositional symmetries in complete genomes. Bioinformatics 17:557-559
    • (2001) Bioinformatics , vol.17 , pp. 557-559
    • Qi, D.1    Cuticchia, J.2
  • 21
    • 0014302250 scopus 로고
    • Separation of B. subtilis DNA into complementary strands. 3. Direct analysis
    • Rudner R, Karkas JD Chargaff.E (1968) Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proc Natl Acad Sci USA 60:921-922
    • (1968) Proc Natl Acad Sci USA , vol.60 , pp. 921-922
    • Rudner, R.1    Karkas Chargaff.e, J.D.2
  • 22
    • 22744442232 scopus 로고    scopus 로고
    • Phylogeny of the centrohelida inferred from SSU rRNA, tubulin, and actin genes
    • Sakagami M, Nakayama T, Hashimoto T, et al (2006) Phylogeny of the centrohelida inferred from SSU rRNA, tubulin, and actin genes. J Mol Evol 61:765-775
    • (2006) J Mol Evol , vol.61 , pp. 765-775
    • Sakagami, M.1    Nakayama, T.2    Hashimoto, T.3
  • 23
    • 33750995860 scopus 로고    scopus 로고
    • The genome of the sea urchin Strongylocentrotus purpurantus
    • Sea urchin genome sequencing consortium
    • Sea urchin genome sequencing consortium (2006) The genome of the sea urchin Strongylocentrotus purpurantus. Science 314:941-952
    • (2006) Science , vol.314 , pp. 941-952
  • 24
    • 0012210873 scopus 로고
    • Evolutionary diversity of eukaryotic small subunit rRNA genes
    • Sogin ML, Elwood HJ, Gunderson H (1986) Evolutionary diversity of eukaryotic small subunit rRNA genes. Proc Natl Acad Sci USA 83:1383-1387
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 1383-1387
    • Sogin, M.L.1    Elwood, H.J.2    Gunderson, H.3
  • 25
    • 0032884548 scopus 로고    scopus 로고
    • Evolutionary changes reflected by the cellular amino acid composition
    • Sorimachi K (1999) Evolutionary changes reflected by the cellular amino acid composition. Amino Acids 17:207-226
    • (1999) Amino Acids , vol.17 , pp. 207-226
    • Sorimachi, K.1
  • 26
    • 0347622548 scopus 로고    scopus 로고
    • Gene assembly consisting of small units with similar amino acid composition in the Saccharomyces cerevisiae genome
    • Sorimachi K, Okayasu T (2003) Gene assembly consisting of small units with similar amino acid composition in the Saccharomyces cerevisiae genome. Mycosicence 44:415-417
    • (2003) Mycosicence , vol.44 , pp. 415-417
    • Sorimachi, K.1    Okayasu, T.2
  • 27
    • 2342578132 scopus 로고    scopus 로고
    • Classification of eubacteria based on their complete genome: Where does Mycoplasmataseae belong?
    • Sorimachi K, Okayasu T (2004a) Classification of eubacteria based on their complete genome: where does Mycoplasmataseae belong? Proc Biol Sci 271:S127-S130
    • (2004) Proc Biol Sci , vol.271
    • Sorimachi, K.1    Okayasu, T.2
  • 28
    • 9744255511 scopus 로고    scopus 로고
    • An evaluation of evolutionary theories based on genomic structures in Saccharomyces cerevisiae and Encephalitozoon cuniculi
    • Sorimachi K, Okayasu T (2004b) An evaluation of evolutionary theories based on genomic structures in Saccharomyces cerevisiae and Encephalitozoon cuniculi. Mycoscience 45:345-350
    • (2004) Mycoscience , vol.45 , pp. 345-350
    • Sorimachi, K.1    Okayasu, T.2
  • 30
    • 0034108711 scopus 로고    scopus 로고
    • Conservation of the basic pattern of cellular amino acid composition during biological evolution in plants
    • Sorimachi K, Okayasu T, Akimoto K, et al (2000) Conservation of the basic pattern of cellular amino acid composition during biological evolution in plants. Amino Acids 18:193-196
    • (2000) Amino Acids , vol.18 , pp. 193-196
    • Sorimachi, K.1    Okayasu, T.2    Akimoto, K.3
  • 31
    • 0035662755 scopus 로고    scopus 로고
    • Conservation of the basic pattern of cellular amino acid composition during biological evolution and the putative amino acid composition of primitive life forms
    • Sorimachi K, Itoh T, Kawarabayasi Y, et al (2001) Conservation of the basic pattern of cellular amino acid composition during biological evolution and the putative amino acid composition of primitive life forms. Amino Acids 21:393-399
    • (2001) Amino Acids , vol.21 , pp. 393-399
    • Sorimachi, K.1    Itoh, T.2    Kawarabayasi, Y.3
  • 32
    • 32844475783 scopus 로고    scopus 로고
    • Mathematical proof of genomic amino acid composition homogeneity based on putative small units
    • Sorimachi K, Okayasu T, Ebara Y, et al (2005) Mathematical proof of genomic amino acid composition homogeneity based on putative small units. Dokkyo J Med Sci 32:99-100
    • (2005) Dokkyo J Med Sci , vol.32 , pp. 99-100
    • Sorimachi, K.1    Okayasu, T.2    Ebara, Y.3
  • 33
    • 0001300503 scopus 로고
    • Correlation between base composition of deoxyribonucleic acid and amino acid composition of proteins
    • Sueoka N (1961) Correlation between base composition of deoxyribonucleic acid and amino acid composition of proteins. Proc Natl Acad Sci USA 47:1141-1149
    • (1961) Proc Natl Acad Sci USA , vol.47 , pp. 1141-1149
    • Sueoka, N.1
  • 34
    • 0028922156 scopus 로고
    • Intrastrand parity rules of DNA base composition and usage biases of synonymous codons
    • Sueoka N (1995) Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol 40:318-325
    • (1995) J Mol Evol , vol.40 , pp. 318-325
    • Sueoka, N.1
  • 35
    • 0033053160 scopus 로고    scopus 로고
    • Two aspects of DNA base composition: G+C content and translation-coupled deviation intra-strand rule of a = T and G = C
    • Sueoka N (1999) Two aspects of DNA base composition: G+C content and translation-coupled deviation intra-strand rule of A = T and G = C. J Mol Evol 49:49-62
    • (1999) J Mol Evol , vol.49 , pp. 49-62
    • Sueoka, N.1
  • 36
    • 0013997435 scopus 로고
    • Pyrimidine clusters on the transcribing strand of DNA and their possible role in the initiation of RNA synthesis
    • Szybalski, Kubinski H, Sheldrick P (1966) Pyrimidine clusters on the transcribing strand of DNA and their possible role in the initiation of RNA synthesis. Cold Spring Harb Symp Quant Biol 31:123-127
    • (1966) Cold Spring Harb Symp Quant Biol , vol.31 , pp. 123-127
    • Szybalski1    Kubinski, H.2    Sheldrick, P.3
  • 37
    • 0027312593 scopus 로고
    • Graphic analysis of codon usage strategy in1490 human proteins
    • Zhang C-T, Chou K-C (1993) Graphic analysis of codon usage strategy in1490 human proteins. J Protein Chem 12:329-335
    • (1993) J Protein Chem , vol.12 , pp. 329-335
    • Zhang, C.-T.1    Chou, K.-C.2
  • 38
    • 0028237028 scopus 로고
    • A graphic approach to analyzing codon usage in 1562 Echerichia coli protein coding sequences
    • Zhang C-T, Chou K-C (1994) A graphic approach to analyzing codon usage in 1562 Echerichia coli protein coding sequences. J Mol Biol 238:1-8
    • (1994) J Mol Biol , vol.238 , pp. 1-8
    • Zhang, C.-T.1    Chou, K.-C.2
  • 39
    • 0029980168 scopus 로고    scopus 로고
    • An analysis of base frequencies in the anti-sense strands corresponding to the 180 human protein coding sequences
    • Zhang C-T, Chou K-C (1996) An analysis of base frequencies in the anti-sense strands corresponding to the 180 human protein coding sequences. Amino Acids 10:253-262
    • (1996) Amino Acids , vol.10 , pp. 253-262
    • Zhang, C.-T.1    Chou, K.-C.2
  • 40
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter JC, et al (2001) The sequence of the human genome. Science 291:304-1351
    • (2001) Science , vol.291 , pp. 304-1351
    • Venter, J.C.1
  • 41
    • 33749048664 scopus 로고
    • Genetical implications of the structure of deoxyribonucleic acid
    • Watson JD, Crick FHC (1953) Genetical implications of the structure of deoxyribonucleic acid. Nature 171:964-967
    • (1953) Nature , vol.171 , pp. 964-967
    • Watson, J.D.1    Crick, F.H.C.2
  • 42
    • 0032499698 scopus 로고    scopus 로고
    • The universal ancestor
    • Woese CR (1998) The universal ancestor. Proc Natl Acad Sci USA 95:6854-6859
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 6854-6859
    • Woese, C.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.