메뉴 건너뛰기




Volumn 7, Issue , 2006, Pages

Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon composition

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID COMPOSITIONS; CLASSIFICATION ACCURACY; DOUBLE-STRAND BREAKS; HIGH FREQUENCY HF; MEIOTIC RECOMBINATIONS; RECOMBINATION RATE; SEQUENCE INFORMATIONS; SVM-BASED METHODS;

EID: 33646692717     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-223     Document Type: Article
Times cited : (26)

References (28)
  • 1
    • 0029587470 scopus 로고
    • Meiotic recombination hotspots
    • Lichten M, Goldman AS: Meiotic recombination hotspots. Annu Rev Genet 1995, 29:423-444.
    • (1995) Annu Rev Genet , vol.29 , pp. 423-444
    • Lichten, M.1    Goldman, A.S.2
  • 2
    • 0034633494 scopus 로고    scopus 로고
    • Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae
    • Gerton JL, DeRisi J, Shroff R, Lichten M, Brown PO, Petes TD: Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2000, 97:11383-11390.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 11383-11390
    • Gerton, J.L.1    DeRisi, J.2    Shroff, R.3    Lichten, M.4    Brown, P.O.5    Petes, T.D.6
  • 3
    • 0031010660 scopus 로고    scopus 로고
    • Clustering of meiotic double-strand breaks on yeast chromosome III
    • Baudat F, Nicolas A: Clustering of meiotic double-strand breaks on yeast chromosome III. Proc Natl Acad Sci USA 1997, 94:5213-5218.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 5213-5218
    • Baudat, F.1    Nicolas, A.2
  • 4
    • 0030460182 scopus 로고    scopus 로고
    • Patterns of meiotic double-strand breakage on native and artificial yeast chromosomes
    • Klein S, Zenvirth D, Dror V, Barton AB, Kaback DB, Simchen G: Patterns of meiotic double-strand breakage on native and artificial yeast chromosomes. Chromosoma 1996, 105:276-84.
    • (1996) Chromosoma , vol.105 , pp. 276-284
    • Klein, S.1    Zenvirth, D.2    Dror, V.3    Barton, A.B.4    Kaback, D.B.5    Simchen, G.6
  • 5
    • 0026658219 scopus 로고
    • Multiple sites for double-strand breaks in whole meiotic chromosomes of Saccharomyces cerevisiae
    • Zenvirth D, Arbel T, Sherman A, Goldway M, Klein S, Simchen G: Multiple sites for double-strand breaks in whole meiotic chromosomes of Saccharomyces cerevisiae. EMBO J 1992, 11:3441-3447.
    • (1992) EMBO J , vol.11 , pp. 3441-3447
    • Zenvirth, D.1    Arbel, T.2    Sherman, A.3    Goldway, M.4    Klein, S.5    Simchen, G.6
  • 6
    • 0041670890 scopus 로고    scopus 로고
    • Selection conflicts, gene expression, and codon usage trends in yeast
    • Kliman RM, Irving N, Santiago M: Selection conflicts, gene expression, and codon usage trends in yeast. J Mol Evol 2003, 57:98-109.
    • (2003) J Mol Evol , vol.57 , pp. 98-109
    • Kliman, R.M.1    Irving, N.2    Santiago, M.3
  • 7
    • 0027383354 scopus 로고
    • Reduced natural selection associated with low recombination in Drosophila melanogaster
    • Kliman RM, Hey J: Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol Biol Evol 1993, 10:1239-1258.
    • (1993) Mol Biol Evol , vol.10 , pp. 1239-1258
    • Kliman, R.M.1    Hey, J.2
  • 8
    • 0035826858 scopus 로고    scopus 로고
    • Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes
    • Marais G, Mouchiroud D, Duret L: Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci USA 2001, 98:5688-5692.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5688-5692
    • Marais, G.1    Mouchiroud, D.2    Duret, L.3
  • 9
    • 0036725703 scopus 로고    scopus 로고
    • Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genome
    • Marais G, Piganeau G: Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genome. Mol Biol Evol 2002, 19:1399-1406.
    • (2002) Mol Biol Evol , vol.19 , pp. 1399-1406
    • Marais, G.1    Piganeau, G.2
  • 10
    • 0033539159 scopus 로고    scopus 로고
    • Evolutionary rate of a gene affected by chromosomal position
    • Perry J, Ashworth A: Evolutionary rate of a gene affected by chromosomal position. Curr Biol 1999, 9:987-989.
    • (1999) Curr Biol , vol.9 , pp. 987-989
    • Perry, J.1    Ashworth, A.2
  • 11
    • 0034989085 scopus 로고    scopus 로고
    • Local rates of recombination are positively correlated with GC content in the human genome
    • Fullerton SM, Bernardo Carvalho A, Clark AG: Local rates of recombination are positively correlated with GC content in the human genome. Mol Biol Evol 2001, 18:1139-1142.
    • (2001) Mol Biol Evol , vol.18 , pp. 1139-1142
    • Fullerton, S.M.1    Bernardo Carvalho, A.2    Clark, A.G.3
  • 12
    • 17444396383 scopus 로고    scopus 로고
    • Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage
    • Friedel CC, Jahn KH, Sommer S, Rudd S, Mewes HW, Tetko IV: Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage. Bioinformatics 2005, 21:1383-1388.
    • (2005) Bioinformatics , vol.21 , pp. 1383-1388
    • Friedel, C.C.1    Jahn, K.H.2    Sommer, S.3    Rudd, S.4    Mewes, H.W.5    Tetko, I.V.6
  • 13
    • 0036606072 scopus 로고    scopus 로고
    • Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: Lessons from supervised machine learning in functional genomics
    • Lin K, Kuang Y, Joseph JS, Kolatkar PR: Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics. Nucleic Acids Res 2002, 30:2599-2607.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2599-2607
    • Lin, K.1    Kuang, Y.2    Joseph, J.S.3    Kolatkar, P.R.4
  • 14
    • 0027043281 scopus 로고
    • Quantile distributions of amino acid usage in protein classes
    • Karlin S, Blaisdell BE, Bucher P: Quantile distributions of amino acid usage in protein classes. Protein Eng 1992, 5:729-38.
    • (1992) Protein Eng , vol.5 , pp. 729-738
    • Karlin, S.1    Blaisdell, B.E.2    Bucher, P.3
  • 15
    • 0031588694 scopus 로고    scopus 로고
    • Relation between amino acid composition and cellular location of proteins
    • Cedano J, Patrick A, PerezPons J, Querol E: Relation between amino acid composition and cellular location of proteins. J Mol Biol 1997, 266:594-600.
    • (1997) J Mol Biol , vol.266 , pp. 594-600
    • Cedano, J.1    Patrick, A.2    PerezPons, J.3    Querol, E.4
  • 16
    • 0028239038 scopus 로고
    • Discrimination of intracellular and extracellular proteins using amino acid compositions and residue-pair frequencies
    • Nakashima H, Nishikawa K: Discrimination of intracellular and extracellular proteins using amino acid compositions and residue-pair frequencies. J Mol Biol 1994, 238:54-61.
    • (1994) J Mol Biol , vol.238 , pp. 54-61
    • Nakashima, H.1    Nishikawa, K.2
  • 17
    • 0023046874 scopus 로고
    • Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes
    • Sharp PM, Tuohy T, Mosurski K, Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 1986, 14:5125-5143.
    • (1986) Nucleic Acids Res , vol.14 , pp. 5125-5143
    • Sharp, P.M.1    Tuohy, T.2    Mosurski, K.3
  • 18
    • 0023650543 scopus 로고
    • The codon adaptation index - A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li WH: The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15:1281-1295.
    • (1987) Nucleic Acids Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 19
    • 0032894285 scopus 로고    scopus 로고
    • Natural selection on synonymous sites is correlated with gene length and recombination rate in Drosophila
    • Comeron JM, Kreitman M, Aguade M: Natural selection on synonymous sites is correlated with gene length and recombination rate in Drosophila. Genetics 1999, 151:239-249.
    • (1999) Genetics , vol.151 , pp. 239-249
    • Comeron, J.M.1    Kreitman, M.2    Aguade, M.3
  • 20
    • 0034099647 scopus 로고    scopus 로고
    • The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation
    • McVean GAT, Charlesworth B: The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 2000, 155:929-944.
    • (2000) Genetics , vol.155 , pp. 929-944
    • McVean, G.A.T.1    Charlesworth, B.2
  • 21
    • 0020024572 scopus 로고
    • Codon selection in yeast
    • Bennetzen JL, Hall BD: Codon selection in yeast. J Biol Chem 1982, 257:3026-3031.
    • (1982) J Biol Chem , vol.257 , pp. 3026-3031
    • Bennetzen, J.L.1    Hall, B.D.2
  • 22
    • 0025988205 scopus 로고
    • Synonymous codon usage in Saccharomyces cerevisiae
    • Sharp PM, Cowe E: Synonymous codon usage in Saccharomyces cerevisiae. Yeast 1991, 7:657-678.
    • (1991) Yeast , vol.7 , pp. 657-678
    • Sharp, P.M.1    Cowe, E.2
  • 23
    • 0036267948 scopus 로고    scopus 로고
    • Cluster analysis of the codon use frequency of MHC genes from different species
    • Ma JM, Zhou T, Gu WJ, Sun X, Lu ZH: Cluster analysis of the codon use frequency of MHC genes from different species. Biosystems 2002, 65:199-207.
    • (2002) Biosystems , vol.65 , pp. 199-207
    • Ma, J.M.1    Zhou, T.2    Gu, W.J.3    Sun, X.4    Lu, Z.H.5
  • 24
    • 0034696628 scopus 로고    scopus 로고
    • A functional significance for codon third bases
    • Richard JE, Lin K, Tan T: A functional significance for codon third bases. Gene 2000, 245:291-298.
    • (2000) Gene , vol.245 , pp. 291-298
    • Richard, J.E.1    Lin, K.2    Tan, T.3
  • 25
    • 84874649471 scopus 로고    scopus 로고
    • Global Mapping of Meiotic Recombination Hotspots and Coldspots in the yeast Saccharomyces cerevisiae
    • Global Mapping of Meiotic Recombination Hotspots and Coldspots in the yeast Saccharomyces cerevisiae [http://derisilab.ucsf.edu/hotspots/]
  • 26
    • 0023046211 scopus 로고
    • Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons
    • Sharp PM, Li WH: Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res 1986, 14:7737-7749.
    • (1986) Nucleic Acids Res , vol.14 , pp. 7737-7749
    • Sharp, P.M.1    Li, W.H.2
  • 28
    • 0000259511 scopus 로고    scopus 로고
    • Approximate statistical tests for comparing supervised classification learning algorithms
    • Dietterich DT: Approximate statistical tests for comparing supervised classification learning algorithms. Neural Comput 1998, 10:1895-1923.
    • (1998) Neural Comput , vol.10 , pp. 1895-1923
    • Dietterich, D.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.