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Volumn 7, Issue 4-5, 2007, Pages 507-526

The CAI Analyser Package: Inferring gene expressivity from raw genomic data

Author keywords

Codon Adaptation Index; Gene expressivity; Intergenomic comparison; Program package; Web server

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BIOINFORMATICS; CLIENT SERVER APPLICATION; CODON ADAPTATION INDEX ANALYSER PACKAGE; CODON USAGE; COMPUTER PROGRAM; ESCHERICHIA COLI; GENE EXPRESSION; GENE SEQUENCE; GENOME ANALYSIS; HELICOBACTER PYLORI; INTERNET; NONHUMAN; SEARCH ENGINE; SEQUENCE ANALYSIS; SPECIES COMPARISON; STATISTICAL ANALYSIS;

EID: 38949176355     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (10)

References (36)
  • 1
    • 0034888743 scopus 로고    scopus 로고
    • Characterizations of highly expressed genes of four fast-growing bacteria
    • Karlin, S., Mrázek, J., Campbell, A. and Kaiser, D. (2001). Characterizations of highly expressed genes of four fast-growing bacteria. J Bacteriol. 183, 5025-5040.
    • (2001) J Bacteriol , vol.183 , pp. 5025-5040
    • Karlin, S.1    Mrázek, J.2    Campbell, A.3    Kaiser, D.4
  • 2
    • 14544277543 scopus 로고    scopus 로고
    • Variation in the strength of selected codon usage bias among bacteria
    • Sharp, P. M., Bailes, E., Grocock, R. J., Peden, J. F. and Sockett, R. E. (2005). Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33, 1141-1153.
    • (2005) Nucleic Acids Res , vol.33 , pp. 1141-1153
    • Sharp, P.M.1    Bailes, E.2    Grocock, R.J.3    Peden, J.F.4    Sockett, R.E.5
  • 3
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optmal for the E. coli translational system
    • Ikernura, T. (1982). Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optmal for the E. coli translational system. J. Mol. Biol. 151, 389-409.
    • (1982) J. Mol. Biol , vol.151 , pp. 389-409
    • Ikernura, T.1
  • 4
    • 8744310123 scopus 로고    scopus 로고
    • Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization
    • Rocha, E. P. (2004). Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res. 14, 2279-2286.
    • (2004) Genome Res , vol.14 , pp. 2279-2286
    • Rocha, E.P.1
  • 5
    • 33845648054 scopus 로고    scopus 로고
    • Error minimization explains the codon usage of highly expressed genes in Escherichia coli
    • Najafabadi, H. S., Lehmann, J. and Omidi, M. (2006). Error minimization explains the codon usage of highly expressed genes in Escherichia coli. Gene 387, 150-155.
    • (2006) Gene , vol.387 , pp. 150-155
    • Najafabadi, H.S.1    Lehmann, J.2    Omidi, M.3
  • 6
    • 33846039881 scopus 로고    scopus 로고
    • Energetics of codon-anticodon recognition on the small ribosomal subunit
    • Almlöf, M., Andér, M. and Aqvist, J. (2007). Energetics of codon-anticodon recognition on the small ribosomal subunit Biochemistry 46, 200-209.
    • (2007) Biochemistry , vol.46 , pp. 200-209
    • Almlöf, M.1    Andér, M.2    Aqvist, J.3
  • 7
    • 14544296732 scopus 로고    scopus 로고
    • Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type- 1
    • Meintjes, P. L. and Rodrigo, A. G. (2005). Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type- 1. J. Bioinform. Comput. Biol. 3, 157-168.
    • (2005) J. Bioinform. Comput. Biol , vol.3 , pp. 157-168
    • Meintjes, P.L.1    Rodrigo, A.G.2
  • 8
    • 0033016717 scopus 로고    scopus 로고
    • Correlation between protein and mRNA abundance in yeast
    • Gygi, S. R, Rochon, Y., Franza, B. R. and Aebersold, R. (1999). Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720-1730.
    • (1999) Mol. Cell. Biol , vol.19 , pp. 1720-1730
    • Gygi, S.R.1    Rochon, Y.2    Franza, B.R.3    Aebersold, R.4
  • 10
    • 0028359705 scopus 로고
    • Codon usage in Caenorhabditis elegans: Delineation of translational selection and mutational biases
    • Stenico, M., Lloyd, A. T. and Sharp, P. M. (1994). Codon usage in Caenorhabditis elegans: Delineation of translational selection and mutational biases. Nucleic Acids Res. 22, 2437-2446.
    • (1994) Nucleic Acids Res , vol.22 , pp. 2437-2446
    • Stenico, M.1    Lloyd, A.T.2    Sharp, P.M.3
  • 11
    • 0034193767 scopus 로고    scopus 로고
    • Studies on codon usage in Entamoeba histolytica
    • Ghosh, T. C., Gupta, S. K. and Majumdar, S. (2000). Studies on codon usage in Entamoeba histolytica. Int J. Parasitol. 30, 715-722.
    • (2000) Int J. Parasitol , vol.30 , pp. 715-722
    • Ghosh, T.C.1    Gupta, S.K.2    Majumdar, S.3
  • 13
    • 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
  • 14
    • 27744507140 scopus 로고    scopus 로고
    • A problem in multivariate analysis of codon usage data and a possible solution
    • Suzuki, H., Saito, R. and Tomita, M. (2005). A problem in multivariate analysis of codon usage data and a possible solution. FEBS Lett. 579 6499-6504.
    • (2005) FEBS Lett , vol.579 , pp. 6499-6504
    • Suzuki, H.1    Saito, R.2    Tomita, M.3
  • 15
    • 0023650543 scopus 로고
    • The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P. M. and Li, W. H. (1987). The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281-1295.
    • (1987) Nucleic Acids Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 16
    • 11144241326 scopus 로고    scopus 로고
    • Correlation of codon bias measures with mRNA levels: Analysis of transcriptome data from Escherichia coli
    • Goetz, R. M.and Fugisang, A. (2005). Correlation of codon bias measures with mRNA levels: Analysis of transcriptome data from Escherichia coli. Biochem. Biophys. Res. Commun. 327, 4-7.
    • (2005) Biochem. Biophys. Res. Commun , vol.327 , pp. 4-7
    • Goetz, R.M.1    Fugisang, A.2
  • 17
    • 33646859041 scopus 로고    scopus 로고
    • A calibration method for estimating absolute expression levels from microarray data
    • Engelen, K, Naudts, B., De Moor, B. and Marchal, K. (2006). A calibration method for estimating absolute expression levels from microarray data. Bioinformatics 22, 1251-1258.
    • (2006) Bioinformatics , vol.22 , pp. 1251-1258
    • Engelen, K.1    Naudts, B.2    De Moor, B.3    Marchal, K.4
  • 18
    • 0942287071 scopus 로고    scopus 로고
    • Comparing expression level-dependent features in codon usage with protein abundance: An analysis of predictive proteomics
    • McHardy, A. C., Pühler, A., Kalinowski, J. and Meyer, F. (2004). Comparing expression level-dependent features in codon usage with protein abundance: An analysis of predictive proteomics'. Proteomics 4, 46-58.
    • (2004) Proteomics , vol.4 , pp. 46-58
    • McHardy, A.C.1    Pühler, A.2    Kalinowski, J.3    Meyer, F.4
  • 19
    • 0242391986 scopus 로고    scopus 로고
    • Codon adaptation index as a measure of dominating codon bias
    • Carbone, A., Zinovyev, A. and Képes, R (2003). Codon adaptation index as a measure of dominating codon bias. Bioinformatics 19, 2005-2015.
    • (2003) Bioinformatics , vol.19 , pp. 2005-2015
    • Carbone, A.1    Zinovyev, A.2    Képes, R.3
  • 20
    • 33646063776 scopus 로고    scopus 로고
    • Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence
    • Wu, G.; Nie, L. and Zhang, W. (2006). Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence. Antonie Van Leeuwenhoek 89, 135-146.
    • (2006) Antonie Van Leeuwenhoek , vol.89 , pp. 135-146
    • Wu, G.1    Nie, L.2    Zhang, W.3
  • 21
    • 22144453213 scopus 로고    scopus 로고
    • Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermutilis and the implications for their metabolism
    • Wu, G., Culley, D. E. and Zhang, W. (2005). Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermutilis and the implications for their metabolism. Microbiology 151, 2175-2187.
    • (2005) Microbiology , vol.151 , pp. 2175-2187
    • Wu, G.1    Culley, D.E.2    Zhang, W.3
  • 22
    • 1542618322 scopus 로고    scopus 로고
    • Codon usage between genomes is constrained by genome-wide mutational processes
    • Chen, S. L., Lee, W., Hottes, A. K., Shapiro, L. and McAdams, H. H. (2004). Codon usage between genomes is constrained by genome-wide mutational processes. Proc. Natl. Acad. Sci. USA 101, 3480-3485.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 3480-3485
    • Chen, S.L.1    Lee, W.2    Hottes, A.K.3    Shapiro, L.4    McAdams, H.H.5
  • 23
    • 0026597059 scopus 로고
    • Codon usage in the G+C-rich Streptomyces genome
    • Wright, F. and Bibb, M. J. (1992). Codon usage in the G+C-rich Streptomyces genome. Gene 113, 55-65.
    • (1992) Gene , vol.113 , pp. 55-65
    • Wright, F.1    Bibb, M.J.2
  • 24
    • 0025283965 scopus 로고
    • Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content
    • Ohama, T., Muto, A, and Osawa, S. (1990). Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content Nucleic Acids Res. 18, 1565-1569.
    • (1990) Nucleic Acids Res , vol.18 , pp. 1565-1569
    • Ohama, T.1    Muto, A.2    Osawa, S.3
  • 25
    • 0025181355 scopus 로고
    • Switches in species-specific codon preferences: The influence of mutation biases
    • Shields, D. C. (1990). Switches in species-specific codon preferences: the influence of mutation biases. J. Mol. Evol. 31, 71-80.
    • (1990) J. Mol. Evol , vol.31 , pp. 71-80
    • Shields, D.C.1
  • 26
    • 34047223024 scopus 로고    scopus 로고
    • Posttranscriptional expression regulation: What determines translation rates?
    • Brockmann, R., Beyer, A., Heinisch, J. J. and Wilhelm T. (2007). Posttranscriptional expression regulation: What determines translation rates? PLoS Comput. Biol. 3, e57.
    • (2007) PLoS Comput. Biol , vol.3
    • Brockmann, R.1    Beyer, A.2    Heinisch, J.J.3    Wilhelm, T.4
  • 28
    • 0342614926 scopus 로고    scopus 로고
    • Codon usage tabulated from international DNA sequence databases: Status for the year 2000
    • Nakamura, Y., Gojobori, T. and 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
  • 29
    • 34547579086 scopus 로고    scopus 로고
    • OPTIMIZER: A web server for optimizing the codon-usage of DNA sequences
    • Puigbò, P., Guzmán, E., Romeu, A. and Garcia-Vallvé, S. (2007). OPTIMIZER: A web server for optimizing the codon-usage of DNA sequences. Nucleic Acids Res. 35, W126-131.
    • (2007) Nucleic Acids Res , vol.35
    • Puigbò, P.1    Guzmán, E.2    Romeu, A.3    Garcia-Vallvé, S.4
  • 30
    • 0344668838 scopus 로고    scopus 로고
    • Gene essentiality determines chromosome organisation in bacteria
    • Rocha, E. P. and Danchin, A. (2003). Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res. 31, 6570-6577.
    • (2003) Nucleic Acids Res , vol.31 , pp. 6570-6577
    • Rocha, E.P.1    Danchin, A.2
  • 31
    • 0032910674 scopus 로고    scopus 로고
    • Universal replication biases in bacteria
    • Rocha, E. P., Danchin, A. and Viari, A. (1999). Universal replication biases in bacteria. Mol. Microbiol. 32, 11-16.
    • (1999) Mol. Microbiol , vol.32 , pp. 11-16
    • Rocha, E.P.1    Danchin, A.2    Viari, A.3
  • 35
    • 33845874641 scopus 로고    scopus 로고
    • Predicting gene expression level from codon usage bias
    • Henry, I. and Sharp, P. M. (2006). Predicting gene expression level from codon usage bias. Mol. Biol. Evol. 24, 10-12.
    • (2006) Mol. Biol. Evol , vol.24 , pp. 10-12
    • Henry, I.1    Sharp, P.M.2
  • 36
    • 0034086295 scopus 로고    scopus 로고
    • Absence of translationatly selected synonymous codon usage bias in Helicobacter pylori
    • Lafay, B., Atherton, J. C. and Sharp, P. M. (2000). Absence of translationatly selected synonymous codon usage bias in Helicobacter pylori. Microbiology 146, 851-860.
    • (2000) Microbiology , vol.146 , pp. 851-860
    • Lafay, B.1    Atherton, J.C.2    Sharp, P.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.