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Volumn 43, Issue 4, 2003, Pages 296-302

PF-IND: Probability algorithm and software for separation of plant and fungal sequences

Author keywords

Codon usage bias; EST; Fungus plant interaction

Indexed keywords

ALGORITHM; ARTICLE; BIOINFORMATICS; CODON; COMPUTER PROGRAM; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; FUNGAL GENE; FUNGAL GENETICS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC SIMILARITY; HOST; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT DISEASE; PLANT FUNGUS INTERACTION; PLANT GENETICS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

EID: 0038302370     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-003-0394-3     Document Type: Article
Times cited : (8)

References (29)
  • 1
    • 0031593202 scopus 로고    scopus 로고
    • Codon bias evolution in Drosophila. Population genetics of mutation-selection drift
    • Akashi H (1997) Codon bias evolution in Drosophila. Population genetics of mutation-selection drift. Gene 205:269-278
    • (1997) Gene , vol.205 , pp. 269-278
    • Akashi, H.1
  • 2
    • 0020024572 scopus 로고
    • Codon selection in yeast
    • Bennetzen J, Hall B (1982) Codon selection in yeast. J Biol Chem 257:3026-3031
    • (1982) J. Biol. Chem. , vol.257 , pp. 3026-3031
    • Bennetzen, J.1    Hall, B.2
  • 3
    • 0344653653 scopus 로고    scopus 로고
    • Codon usage and gene function are related in sequences of Arabidopsis thaliana
    • Chiapello H, Lisacek F, Caboche M, Henaut A (1998) Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene 209:GC1-GC38
    • (1998) Gene , vol.209
    • Chiapello, H.1    Lisacek, F.2    Caboche, M.3    Henaut, A.4
  • 4
    • 0034666040 scopus 로고    scopus 로고
    • Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
    • Coghlan A, Wolfe K (2000) Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16:1131-1145
    • (2000) Yeast , vol.16 , pp. 1131-1145
    • Coghlan, A.1    Wolfe, K.2
  • 5
    • 0031694427 scopus 로고    scopus 로고
    • An evaluation of measures of synonymous codon usage bias
    • Comeron J, Aguade M (1998) An evaluation of measures of synonymous codon usage bias. J Mol Evol 47:268-274
    • (1998) J. Mol. Evol. , vol.47 , pp. 268-274
    • Comeron, J.1    Aguade, M.2
  • 6
    • 0035150079 scopus 로고    scopus 로고
    • Synonymous codon usage in bacteria
    • Ermolaeva M (2001) Synonymous codon usage in bacteria. Curr Issues Mol Biol 3:91-97
    • (2001) Curr. Issues Mol. Biol. , vol.3 , pp. 91-97
    • Ermolaeva, M.1
  • 7
    • 0027525640 scopus 로고
    • Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C- and G-ending codons
    • Fennoy S, Bailey-Serres J (1993) Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C- and G-ending codons. Nucleic Acids Res 21:5294-5300
    • (1993) Nucleic Acids Res. , vol.21 , pp. 5294-5300
    • Fennoy, S.1    Bailey-Serres, J.2
  • 9
    • 0033136714 scopus 로고    scopus 로고
    • Identification of disease response genes expressed in Gossypium hirsutum upon infection with the wilt pathogen Verticillium dahliae
    • Hill M, Lyon K, Lyon B (1999) Identification of disease response genes expressed in Gossypium hirsutum upon infection with the wilt pathogen Verticillium dahliae. Plant Mol Biol 40:289-296
    • (1999) Plant Mol. Biol. , vol.40 , pp. 289-296
    • Hill, M.1    Lyon, K.2    Lyon, B.3
  • 10
    • 0033212946 scopus 로고    scopus 로고
    • Increased expression of a plant actin gene during a biotrophic interaction between round-leaved mallow, Malva pusilla, and Colletotrichum gloeosporioides f. sp. malvae
    • Jin S, Xu R, Wei Y, Goodwin P (1999) Increased expression of a plant actin gene during a biotrophic interaction between round-leaved mallow, Malva pusilla, and Colletotrichum gloeosporioides f. sp. malvae. Planta 209:487-494
    • (1999) Planta , vol.209 , pp. 487-494
    • Jin, S.1    Xu, R.2    Wei, Y.3    Goodwin, P.4
  • 11
    • 0035802405 scopus 로고    scopus 로고
    • Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): Characterization of horizontally transferred genes with emphasis on the E. coli O157 genome
    • Kanaya S, Kinouchi M, Abe T, Kudo Y, Yamada Y, Nishi T, Mori H, Ikemura T (2001) Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene 276:89-99
    • (2001) Gene , vol.276 , pp. 89-99
    • Kanaya, S.1    Kinouchi, M.2    Abe, T.3    Kudo, Y.4    Yamada, Y.5    Nishi, T.6    Mori, H.7    Ikemura, T.8
  • 12
    • 0035399931 scopus 로고    scopus 로고
    • Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
    • Karlin S (2001) Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol 9:335-343
    • (2001) Trends Microbiol. , vol.9 , pp. 335-343
    • Karlin, S.1
  • 13
    • 0036010853 scopus 로고    scopus 로고
    • A thaumatin-like gene in nonclimacteric pepper fruits used as molecular marker in probing disease resistance, ripening, and sugar accumulation
    • Kim Y, Park J, Kim K, Ko M, Cheong S, Oh B (2002) A thaumatin-like gene in nonclimacteric pepper fruits used as molecular marker in probing disease resistance, ripening, and sugar accumulation. Plant Mol Biol 49:125-135
    • (2002) Plant Mol. Biol. , vol.49 , pp. 125-135
    • Kim, Y.1    Park, J.2    Kim, K.3    Ko, M.4    Cheong, S.5    Oh, B.6
  • 14
    • 0035991175 scopus 로고    scopus 로고
    • Functional and comparative bioinformatic analysis of expressed genes from wheat spikes infected with Fusarium graminearum
    • Kruger W, Pritsch C, Chao S, Muehlbauer G (2002) Functional and comparative bioinformatic analysis of expressed genes from wheat spikes infected with Fusarium graminearum. Mol Plant-Microbe Interact 15:445-455
    • (2002) Mol. Plant-Microbe Interact. , vol.15 , pp. 445-455
    • Kruger, W.1    Pritsch, C.2    Chao, S.3    Muehlbauer, G.4
  • 15
    • 0036193136 scopus 로고    scopus 로고
    • Identification of a hydrophobin gene that is developmentally regulated in the ectomycorrhizal fungus Tricholoma terreum
    • Mankel A, Krause K, Kothe E (2002) Identification of a hydrophobin gene that is developmentally regulated in the ectomycorrhizal fungus Tricholoma terreum. Appl Environ Microbiol 68:1408-1413
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 1408-1413
    • Mankel, A.1    Krause, K.2    Kothe, E.3
  • 16
    • 0032215658 scopus 로고    scopus 로고
    • Cloning, sequence and characterization of a sunflower (Helianthus annuus L.) pathogen-induced gene showing sequence homology with auxin-induced genes from plants
    • Mazeyrat F, Mouzeyar S, Nicolas P, Tourvieille de Labrouhe D, Ledoigt G (1998) Cloning, sequence and characterization of a sunflower (Helianthus annuus L.) pathogen-induced gene showing sequence homology with auxin-induced genes from plants. Plant Mol Biol 38:899-903
    • (1998) Plant Mol. Biol. , vol.38 , pp. 899-903
    • Mazeyrat, F.1    Mouzeyar, S.2    Nicolas, P.3    Tourvieille de Labrouhe, D.4    Ledoigt, G.5
  • 17
    • 0030731696 scopus 로고    scopus 로고
    • Codon usage bias and tRNA abundance in Drosophila
    • Moriyama E, Powell J (1997) Codon usage bias and tRNA abundance in Drosophila. J Mol Evol 45:514-523
    • (1997) J. Mol. Evol. , vol.45 , pp. 514-523
    • Moriyama, E.1    Powell, J.2
  • 18
    • 0032126484 scopus 로고    scopus 로고
    • Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli
    • Moriyama E, Powell J (1998) Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli. Nucleic Acids Res 26:3188-3193
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3188-3193
    • Moriyama, E.1    Powell, J.2
  • 19
    • 0032870941 scopus 로고    scopus 로고
    • Codon usage and lateral gene transfer in Bacillus subtilis
    • Moszer I, Rocha E, Danchin A (1999) Codon usage and lateral gene transfer in Bacillus subtilis. Curr Opin Microbiol 2:524-528
    • (1999) Curr. Opin. Microbiol. , vol.2 , pp. 524-528
    • Moszer, I.1    Rocha, E.2    Danchin, A.3
  • 20
    • 0342614926 scopus 로고    scopus 로고
    • Codon usage tabulated from international DNA sequence databases: Status for the year 2000
    • Nakamura Y, Gojobori T, Ikemura T (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res 28:292
    • (2000) Nucleic Acids Res. , vol.28 , pp. 292
    • Nakamura, Y.1    Gojobori, T.2    Ikemura, T.3
  • 21
    • 0030861159 scopus 로고    scopus 로고
    • Evolution of codon usage bias in Drosophila
    • Powell J, Moriyama E (1997) Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA 94:7784-7790
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 7784-7790
    • Powell, J.1    Moriyama, E.2
  • 22
    • 0032420118 scopus 로고    scopus 로고
    • Cloning of genes by mRNA differential display induced during the hypersensitive reaction of soybean after inoculation with Pseudomonas syringae pv. glycinea
    • Seehaus K, Tenhaken R (1998) Cloning of genes by mRNA differential display induced during the hypersensitive reaction of soybean after inoculation with Pseudomonas syringae pv. glycinea. Plant Mol Biol 38:1225-1234
    • (1998) Plant Mol. Biol. , vol.38 , pp. 1225-1234
    • Seehaus, K.1    Tenhaken, R.2
  • 23
    • 0023650543 scopus 로고
    • The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp P, Li W (1987) The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281-1395
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1395
    • Sharp, P.1    Li, W.2
  • 24
    • 0030878527 scopus 로고    scopus 로고
    • The majority of long non-stop reading frames on the antisense strand can be explained by biased codon usage
    • Silke J (1997) The majority of long non-stop reading frames on the antisense strand can be explained by biased codon usage. Gene 194:143-155
    • (1997) Gene , vol.194 , pp. 143-155
    • Silke, J.1
  • 25
    • 0035040364 scopus 로고    scopus 로고
    • Analysis of codon usage patterns of bacterial genomes using the self-organizing map
    • Wang H, Badger J, Kearney P, Mo L (2001) Analysis of codon usage patterns of bacterial genomes using the self-organizing map. Mol Biol Evol 18:792-800
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 792-800
    • Wang, H.1    Badger, J.2    Kearney, P.3    Mo, L.4
  • 26
    • 0034961863 scopus 로고    scopus 로고
    • Analysis of the codon usage pattern in the Vibrio cholerae genome
    • Wang J, Zhang C (2001) Analysis of the codon usage pattern in the Vibrio cholerae genome. J Biomol Struct Dyn 18:872-880
    • (2001) J. Biomol. Struct. Dyn. , vol.18 , pp. 872-880
    • Wang, J.1    Zhang, C.2
  • 27
    • 0031724888 scopus 로고    scopus 로고
    • A simple program to calculate codon bias index
    • Wang T, Cheng W, Lee B (1998) A simple program to calculate codon bias index. Mol Biotechnol 10:103-106
    • (1998) Mol. Biotechnol. , vol.10 , pp. 103-106
    • Wang, T.1    Cheng, W.2    Lee, B.3
  • 28
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • Wright F (1990) The 'effective number of codons' used in a gene. Gene 87:23-29
    • (1990) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 29
    • 0036112574 scopus 로고    scopus 로고
    • Time for a blast: Genomics of Magnaporthe grisea
    • Xu J, Xue C (2002) Time for a blast: genomics of Magnaporthe grisea. Mol Plant Pathol 3:173-176
    • (2002) Mol. Plant. Pathol. , vol.3 , pp. 173-176
    • Xu, J.1    Xue, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.