메뉴 건너뛰기




Volumn 25, Issue 23, 2009, Pages 3077-3083

Detection of new protein domains using co-occurrence: Application to Plasmodium falciparum

Author keywords

[No Author keywords available]

Indexed keywords

PLASMODIUM FALCIPARUM;

EID: 75949115003     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp560     Document Type: Article
Times cited : (29)

References (29)
  • 1
    • 0035816218 scopus 로고    scopus 로고
    • Domain combinations in archaeal, eubacterial and eukaryotic proteomes
    • Apic, G. et al. (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol., 310, 311-325.
    • (2001) J. Mol. Biol. , vol.310 , pp. 311-325
    • Apic, G.1
  • 2
    • 0037246674 scopus 로고    scopus 로고
    • Plasmodb: the plasmodium genome resource. a database integrating experimental and computational data
    • Bahl, A. et al. (2003) Plasmodb: the plasmodium genome resource. a database integrating experimental and computational data. Nucleic Acids Res., 31, 212-215.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 212-215
    • Bahl, A.1
  • 3
    • 18144420835 scopus 로고    scopus 로고
    • Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions
    • Bastien, O. et al. (2005) Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions. C.R. Biol., 328, 445-453.
    • (2005) C. R. Biol. , vol.328 , pp. 445-453
    • Bastien, O.1
  • 4
    • 34547914091 scopus 로고    scopus 로고
    • Automated improvement of domain annotations using context analysis of domain arrangements (aidan)
    • Beaussart, F. et al. (2007)Automated improvement of domain annotations using context analysis of domain arrangements (aidan). Bioinformatics, 23, 1834-1836.
    • (2007) Bioinformatics , vol.23 , pp. 1834-1836
    • Beaussart, F.1
  • 5
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J.R. Stat. Soc., 85, 289-300.
    • (1995) J. R. Stat. Soc. , vol.85 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 6
    • 25444456367 scopus 로고    scopus 로고
    • Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eucaryotes
    • Callebaut, I. et al. (2005) Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eucaryotes. BMC Genomics, 6, 100.
    • (2005) BMC Genomics , vol.6 , pp. 100
    • Callebaut, I.1
  • 7
    • 34447506247 scopus 로고    scopus 로고
    • Comprehensive analysis of co-occurring domain sets in yeast proteins
    • Cohen-Gihon, I. et al. (2007) Comprehensive analysis of co-occurring domain sets in yeast proteins. BMC Genomics, 8, 161.
    • (2007) BMC Genomics , vol.8 , pp. 161
    • Cohen-Gihon, I.1
  • 8
    • 0037446851 scopus 로고    scopus 로고
    • Enhanced protein domain discovery by using language modeling techniques from speech recognition
    • Coin, L. et al. (2003) Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc. Natl Acad. Sci. USA, 100, 4516-4520.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 4516-4520
    • Coin, L.1
  • 9
    • 4444339460 scopus 로고    scopus 로고
    • Comparative genomics of transcriptional control in the human parasite Plasmodium falciparum
    • Coulson, R. et al. (2004) Comparative genomics of transcriptional control in the human parasite Plasmodium falciparum. Genome Res., 14, 1548-1554.
    • (2004) Genome Res. , vol.14 , pp. 1548-1554
    • Coulson, R.1
  • 10
    • 0003516147 scopus 로고    scopus 로고
    • Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
    • Cambridge University Press, Cambridge, UK
    • Durbin, R. et al. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
    • (1998)
    • Durbin, R.1
  • 11
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.1
  • 12
    • 38549146894 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Finn, R. et al. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-D288.
    • (2008) Nucleic Acids Res. , vol.36
    • Finn, R.1
  • 13
    • 48249113702 scopus 로고    scopus 로고
    • Predicting protein function from domain content
    • Forslund, K. and Sonnhammer, E. (2008) Predicting protein function from domain content. Bioinformatics, 24, 1681-1687.
    • (2008) Bioinformatics , vol.24 , pp. 1681-1687
    • Forslund, K.1    Sonnhammer, E.2
  • 14
    • 0036796467 scopus 로고    scopus 로고
    • CDART: protein homology by domain architecture
    • Geer, L. et al. (2002) CDART: protein homology by domain architecture. Genome Res., 12, 1619-1623.
    • (2002) Genome Res. , vol.12 , pp. 1619-1623
    • Geer, L.1
  • 15
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology
    • Gene Ontology Consortium
    • Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
  • 16
    • 0034767547 scopus 로고    scopus 로고
    • Annotation transfer for genomics: measuring functional divergence in multi-domain proteins
    • Gerstein, M. and Hegyi, H. (2001) Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res., 11, 1632-1640.
    • (2001) Genome Res. , vol.11 , pp. 1632-1640
    • Gerstein, M.1    Hegyi, H.2
  • 17
    • 0040982083 scopus 로고    scopus 로고
    • A plastid of probable green algal origin in Apicomplexan parasites
    • Kohler, S. et al. (1997) A plastid of probable green algal origin in Apicomplexan parasites. Science, 275, 1485-1489.
    • (1997) Science , vol.275 , pp. 1485-1489
    • Kohler, S.1
  • 19
    • 37549035873 scopus 로고    scopus 로고
    • On the detection of functionally coherent groups of protein domains with an extension to protein annotation
    • McLaughlin, W. et al. (2007) On the detection of functionally coherent groups of protein domains with an extension to protein annotation. BMC Bioinformatics, 8, 390.
    • (2007) BMC Bioinformatics , vol.8 , pp. 390
    • McLaughlin, W.1
  • 20
    • 33846116032 scopus 로고    scopus 로고
    • New developments in the interpro database
    • Mulder, N. et al. (2007) New developments in the interpro database. Nucleic Acid Res., 35, D224-D228.
    • (2007) Nucleic Acid Res. , vol.35
    • Mulder, N.1
  • 21
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.1
  • 22
    • 0035104190 scopus 로고    scopus 로고
    • Low-complexity regions in plasmodium falciparum proteins
    • Pizzi, E. and Frontali, C. (2001) Low-complexity regions in plasmodium falciparum proteins. Genome Res., 11, 218-229.
    • (2001) Genome Res. , vol.11 , pp. 218-229
    • Pizzi, E.1    Frontali, C.2
  • 23
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: an application for the Monte Carlo simulation of dna sequence evolution along phylogenetic trees
    • Rambaut, A. and Grassly, N. (1997) Seq-Gen: an application for the Monte Carlo simulation of dna sequence evolution along phylogenetic trees. Comput. Appl. Biosci., 13, 235-238.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.2
  • 24
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson, J. (1981) The anatomy and taxonomy of protein structure. Adv. Protein Chem., 34, 167-339.
    • (1981) Adv. Protein Chem. , vol.34 , pp. 167-339
    • Richardson, J.1
  • 25
    • 6344283102 scopus 로고    scopus 로고
    • Predicting subcellular localization via protein motif co-occurrence
    • Scott, M. et al. (2004) Predicting subcellular localization via protein motif co-occurrence. Genome Res., 14, 1957-1966.
    • (2004) Genome Res. , vol.14 , pp. 1957-1966
    • Scott, M.1
  • 26
    • 0000453490 scopus 로고
    • Statistical 'discoveries' and effect size estimation
    • Soriç, B. (1989) Statistical 'discoveries' and effect size estimation. J. Am. Stat. Assoc., 84, 608-610.
    • (1989) J. Am. Stat. Assoc. , vol.84 , pp. 608-610
    • Soriç, B.1
  • 27
    • 58149191270 scopus 로고    scopus 로고
    • The universal protein resource (UniProt) 2009
    • UniProt Consortium
    • UniProt Consortium (2009) The universal protein resource (UniProt) 2009. Nucleic Acids Res., 37, D169-D174.
    • (2009) Nucleic Acids Res. , vol.37
  • 28
    • 33646268799 scopus 로고    scopus 로고
    • Domain deletions and substitutions in the modular protein evolution
    • Weiner, J. 3rd et al. (2006) Domain deletions and substitutions in the modular protein evolution. FEBS J., 273, 2037-2047.
    • (2006) FEBS J. , vol.273 , pp. 2037-2047
    • Weiner J. III1
  • 29
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan, S. and Goldman, N. (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol., 18, 691-699.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.