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Volumn 22, Issue 9, 2006, Pages 1055-1063

A novel sensitive method for the detection of user-defined compositional bias in biological sequences

Author keywords

[No Author keywords available]

Indexed keywords

COLLAGEN; COMPLEMENTARY DNA; CYTOCHROME C; MYC PROTEIN; PRION PROTEIN; RIBOSOME PROTEIN; SERINE TRANSFER RNA LIGASE;

EID: 33646187499     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl049     Document Type: Article
Times cited : (16)

References (33)
  • 1
    • 0036080338 scopus 로고    scopus 로고
    • Detecting cryptically simple protein sequences using the SIMPLE algorithm
    • Alba,M.M. et al. (2002) Detecting cryptically simple protein sequences using the SIMPLE algorithm. Bioinformatics, 8, 672-678.
    • (2002) Bioinformatics , vol.8 , pp. 672-678
    • Alba, M.M.1
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 3
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology consortium
    • Ashburner,M. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology consortium. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 4
    • 0033957834 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 45-48
    • Bairoch, A.1    Apweiler, R.2
  • 5
    • 0031657823 scopus 로고    scopus 로고
    • Supercoiled protein motifs: The collagen triple-helix and the alpha-helical coiled coil
    • Beck,K. and Brodsky,B. (1998) Supercoiled protein motifs: The collagen triple-helix and the alpha-helical coiled coil. J. Struct. Biol., 122, 17-29.
    • (1998) J. Struct. Biol. , vol.122 , pp. 17-29
    • Beck, K.1    Brodsky, B.2
  • 6
    • 0032974859 scopus 로고    scopus 로고
    • Amino acid composition of protein termini are biased in different manners
    • Berezovsky,I.N. et al. (1999) Amino acid composition of protein termini are biased in different manners. Protein Eng., 12, 23-30.
    • (1999) Protein Eng. , vol.12 , pp. 23-30
    • Berezovsky, I.N.1
  • 7
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman,H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 8
    • 0005588343 scopus 로고
    • Association of charge clusters with functional domains of cellular transcription factors
    • Brendel,V. and Karlin,S. (1989) Association of charge clusters with functional domains of cellular transcription factors. Proc. Natl Acad. Sci. USA, 86, 5698-5702.
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 5698-5702
    • Brendel, V.1    Karlin, S.2
  • 9
    • 0026520770 scopus 로고
    • Methods and algorithms for statistical analysis of protein sequences
    • Brendel,V. et al. (1992) Methods and algorithms for statistical analysis of protein sequences. Proc. Natl Acad. Sci. USA, 89, 2002-2006.
    • (1992) Proc Natl Acad. Sci. USA , vol.89 , pp. 2002-2006
    • Brendel, V.1
  • 10
    • 0032993447 scopus 로고    scopus 로고
    • Polymer principles and protein folding
    • Dill,K.A. (1999) Polymer principles and protein folding. Protein Sci., 8, 1166-1180.
    • (1999) Protein Sci. , vol.8 , pp. 1166-1180
    • Dill, K.A.1
  • 11
    • 0027491528 scopus 로고
    • Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 Å resolution
    • Fujinaga,M. et al. (1993) Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 Å resolution. J. Mol. Biol., 234, 222-233.
    • (1993) J. Mol. Biol. , vol.234 , pp. 222-233
    • Fujinaga, M.1
  • 12
    • 12744257602 scopus 로고    scopus 로고
    • Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum
    • Gardner,M.J. et al. (1998) Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science, 282, 1126-1132.
    • (1998) Science , vol.282 , pp. 1126-1132
    • Gardner, M.J.1
  • 14
    • 0038576863 scopus 로고    scopus 로고
    • A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes
    • Harrison,P.M. and Gerstein,M. (2003) A method to assess compositional bias in biological sequences and its application to prion-like glutamine/ asparagine-rich domains in eukaryotic proteomes. Genome Biol., 4, R40.
    • (2003) Genome Biol. , vol.4
    • Harrison, P.M.1    Gerstein, M.2
  • 15
    • 0033845697 scopus 로고    scopus 로고
    • Evolution of simple sequence in proteins
    • Huntley,M. and Golding,G.B. (2000.) Evolution of simple sequence in proteins. J. Mol. Evol, 51, 131-140.
    • (2000) J. Mol. Evol , vol.51 , pp. 131-140
    • Huntley, M.1    Golding, G.B.2
  • 16
    • 0036643433 scopus 로고    scopus 로고
    • Simple sequences are rare in the Protein Data Bank
    • Huntley,M.A. and Golding,G.B. (2002) Simple sequences are rare in the Protein Data Bank. Proteins, 48, 134-140.
    • (2002) Proteins , vol.48 , pp. 134-140
    • Huntley, M.A.1    Golding, G.B.2
  • 17
    • 0029983147 scopus 로고    scopus 로고
    • Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development
    • Karlin,S. and Burge,C. (1996) Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development. Proc. Natl Acad. Sci. USA, 93, 1560-1565.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 1560-1565
    • Karlin, S.1    Burge, C.2
  • 18
    • 0025275577 scopus 로고
    • Identification of significant sequence patterns in proteins
    • Karlin,S. et al. (1990) Identification of significant sequence patterns in proteins. Methods Enzymol., 183, 388-402.
    • (1990) Methods Enzymol. , vol.183 , pp. 388-402
    • Karlin, S.1
  • 19
    • 0037039436 scopus 로고    scopus 로고
    • Amino acid rums in eukaryotic proteomes and disease associations
    • Karlin,S. et al. (2002) Amino acid rums in eukaryotic proteomes and disease associations. Proc. Natl Acad. Sci. USA, 99, 333-338.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 333-338
    • Karlin, S.1
  • 20
    • 0037494681 scopus 로고    scopus 로고
    • Genome comparisons and analysis
    • Karlin,S. et al. (2003) Genome comparisons and analysis. Curr. Opin. Struct. Biol., 13, 344-352.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 344-352
    • Karlin, S.1
  • 21
    • 0035423087 scopus 로고    scopus 로고
    • The kink-turn: A new RNA secondary structure motif
    • Klein,D.J. et al. (2001) The kink-turn: A new RNA secondary structure motif. EMBO J., 20, 4214-4221.
    • (2001) EMBO J. , vol.20 , pp. 4214-4221
    • Klein, D.J.1
  • 22
    • 0034869693 scopus 로고    scopus 로고
    • Crystal structure of the human prion protein reveals a mechanism for oligomerization
    • Knaus,K.J. et al. (2001) Crystal structure of the human prion protein reveals a mechanism for oligomerization. Nat. Struct. Biol., 8, 770-774.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 770-774
    • Knaus, K.J.1
  • 23
    • 0141738778 scopus 로고    scopus 로고
    • Comparison of sequence masking algorithms and the detection of biased protein sequence regions
    • Kreil,D.P. and Ouzounis,C.A. (2003) Comparison of sequence masking algorithms and the detection of biased protein sequence regions. Bioinformatics, 19, 1672-1681.
    • (2003) Bioinformatics , vol.19 , pp. 1672-1681
    • Kreil, D.P.1    Ouzounis, C.A.2
  • 24
    • 0033080811 scopus 로고    scopus 로고
    • Trafficking of the cellular isoform of the prion protein
    • Lehmann,S. et al. (1999) Trafficking of the cellular isoform of the prion protein. Biomed. Pharmacother., 53, 39-46.
    • (1999) Biomed. Pharmacother. , vol.53 , pp. 39-46
    • Lehmann, S.1
  • 25
    • 0036169928 scopus 로고    scopus 로고
    • Tolerating some redundancy significantly speeds up clustering of large protein databases
    • Li,W. et al. (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics, 8, 77-82.
    • (2002) Bioinformatics , vol.8 , pp. 77-82
    • Li, W.1
  • 26
    • 0031686868 scopus 로고    scopus 로고
    • Biased usages of arginines and lysines in proteins are correlated with local-scale fluctuations of the G + C content of DNA sequences
    • Nishizawa,M. and Nishizawa,K. (1998) Biased usages of arginines and lysines in proteins are correlated with local-scale fluctuations of the G + C content of DNA sequences. J. Mol. Evol., 47, 385-393.
    • (1998) J. Mol. Evol. , vol.47 , pp. 385-393
    • Nishizawa, M.1    Nishizawa, K.2
  • 27
    • 0033638015 scopus 로고    scopus 로고
    • CAST: An iterative algorithm for the complexity analysis of sequence tracts
    • Promponas,V.J. et al. (2000) CAST: An iterative algorithm for the complexity analysis of sequence tracts. Bioinformatics, 16, 915-922.
    • (2000) Bioinformatics , vol.16 , pp. 915-922
    • Promponas, V.J.1
  • 29
    • 12144267492 scopus 로고    scopus 로고
    • Underlying hydrophobic sequence periodicity of protein tertiary structure
    • Silverman,B.D. (2005) Underlying hydrophobic sequence periodicity of protein tertiary structure. J. Biomol. Struct. Dyn., 22, 411-423.
    • (2005) J. Biomol. Struct. Dyn. , vol.22 , pp. 411-423
    • Silverman, B.D.1
  • 30
    • 0033745103 scopus 로고    scopus 로고
    • Nucleotide bias causes a genome wide bias in the amino acid composition of proteins
    • Singer,G.A. and Hickey,D.A. (2000) Nucleotide bias causes a genome wide bias in the amino acid composition of proteins. Mol. Biol. Evol., 17, 1581-1588.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1581-1588
    • Singer, G.A.1    Hickey, D.A.2
  • 31
    • 11244338080 scopus 로고    scopus 로고
    • C-type cytochrome formation: Chemical and biological enigmas
    • Stevens,J.M. et al. (2004) C-type cytochrome formation: Chemical and biological enigmas. Acc. Chem. Res., 37, 999-1007.
    • (2004) Acc. Chem. Res. , vol.37 , pp. 999-1007
    • Stevens, J.M.1
  • 32
    • 0024832782 scopus 로고
    • Differential expression of two Xenopus c-myc proto-oncogenes during development
    • Vriz,S. et al. (1989) Differential expression of two Xenopus c-myc proto-oncogenes during development. EMBO J., 8, 4091-4097.
    • (1989) EMBO J. , vol.8 , pp. 4091-4097
    • Vriz, S.1
  • 33
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.
    • (1996) Methods Enzymol. , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2


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