메뉴 건너뛰기




Volumn 19, Issue 6, 2003, Pages 717-726

Evaluation of annotation strategies using an entire genome sequence

(23)  Iliopoulos, Ioannis a,j   Tsoka, Sophia a   Andrade, Miguel A b,c   Enright, Anton J a,k   Carroll, Mark a,l   Poullet, Patrick a,m   Promponas, Vassilis d   Liakopoulos, Theodore d   Palaios, Giorgos d   Pasquier, Claude d,n   Hamodrakas, Stavros d   Tamames, Javier e,o   Yagnik, Asutosh T e,p   Tramontano, Anna e,q   Devos, Damien f   Blaschke, Christian f   Valencia, Alfonso f   Brett, David c,r   Martin, David g,s   Leroy, Christophe h   more..

e IRBM   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTICAL ERROR; ANIMAL CELL; ARTICLE; AUTOMATION; CHLAMYDIA TRACHOMATIS; CONTROLLED STUDY; DATA ANALYSIS; DOCUMENTATION; EXPERT SYSTEM; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; INFORMATION PROCESSING; INTERMETHOD COMPARISON; METHODOLOGY; NONHUMAN; PRIORITY JOURNAL; RATING SCALE; REPRODUCIBILITY; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEROTYPE;

EID: 0037433717     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg077     Document Type: Article
Times cited : (64)

References (37)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z. 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    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 2
    • 0030760547 scopus 로고    scopus 로고
    • Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function
    • Andrade,M., Casari,G., de Daruvar,A., Sander,C., Schneider,R. et al. (1997) Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. Comput. Appl. Biosci., 13, 481-483.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 481-483
    • Andrade, M.1    Casari, G.2    de Daruvar, A.3    Sander, C.4    Schneider, R.5
  • 5
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • Brenner,S.E. (1999) Errors in genome annotation. Trends Genet., 15, 132-133.
    • (1999) Trends Genet. , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 7
    • 0024444329 scopus 로고
    • Evolution of a biosynthetic pathway: The tryptophan paradigm
    • Crawford,I.P. (1989) Evolution of a biosynthetic pathway: the tryptophan paradigm. Annu. Rev. Microbiol., 43, 567-600.
    • (1989) Annu. Rev. Microbiol. , vol.43 , pp. 567-600
    • Crawford, I.P.1
  • 10
    • 0035327167 scopus 로고    scopus 로고
    • DELPHI: A pattern-based method for detecting sequence similarity
    • Floratos,A., Rigoutsos,I., Parida,L. and Gao,Y. (2001) DELPHI: a pattern-based method for detecting sequence similarity. IBM J. Res. Dev., 45.
    • (2001) IBM J. Res. Dev. , vol.45
    • Floratos, A.1    Rigoutsos, I.2    Parida, L.3    Gao, Y.4
  • 12
    • 0342751307 scopus 로고    scopus 로고
    • Regulation of the cnr cobalt and nickel resistance determinant from Ralstonia sp. strain CH34
    • Grass,G., Grosse,C. and Nies,D.H. (2000) Regulation of the cnr cobalt and nickel resistance determinant from Ralstonia sp. strain CH34. J. Bacteriol., 182, 1390-1398.
    • (2000) J. Bacteriol. , vol.182 , pp. 1390-1398
    • Grass, G.1    Grosse, C.2    Nies, D.H.3
  • 14
    • 0032953228 scopus 로고    scopus 로고
    • Comparative genomes of Chlamydia pneumoniae and C. trachomatis
    • Kalman,S., Mitchell,W., Marathe,R., Lammel,C., Fan,J. et al. (1999) Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat. Genet., 21, 385-389.
    • (1999) Nat. Genet. , vol.21 , pp. 385-389
    • Kalman, S.1    Mitchell, W.2    Marathe, R.3    Lammel, C.4    Fan, J.5
  • 15
    • 0031797096 scopus 로고    scopus 로고
    • What we do not know about sequence analysis and sequence databases
    • [editorial]
    • Karp,P.D. (1998) What we do not know about sequence analysis and sequence databases [editorial]. Bioinformatics, 14, 753-754.
    • (1998) Bioinformatics , vol.14 , pp. 753-754
    • Karp, P.D.1
  • 16
    • 0030868589 scopus 로고    scopus 로고
    • Comparison of archaeal and bacterial genomes: Computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
    • Koonin,E.V., Mushegian,A.R., Galperin,M.Y. and Walker,D.R. (1997) Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol. Microbiol., 25, 619-637.
    • (1997) Mol. Microbiol. , vol.25 , pp. 619-637
    • Koonin, E.V.1    Mushegian, A.R.2    Galperin, M.Y.3    Walker, D.R.4
  • 17
    • 0001602527 scopus 로고    scopus 로고
    • Alternative splicing results in differential expression, activity, and localization of the two forms of arginyl-tRNA-protein transferase, a component of the N-end rule pathway
    • Kwon,Y.T., Kashina,A.S. and Varshavsky,A. (1999) Alternative splicing results in differential expression, activity, and localization of the two forms of arginyl-tRNA-protein transferase, a component of the N-end rule pathway. Mol. Cell Biol., 19, 182-193.
    • (1999) Mol. Cell Biol. , vol.19 , pp. 182-193
    • Kwon, Y.T.1    Kashina, A.S.2    Varshavsky, A.3
  • 18
    • 0032873141 scopus 로고    scopus 로고
    • Genomes OnLine Database (GOLD 1.0): A monitor of complete and ongoing genome projects world-wide
    • Kyrpides,N.C. (1999) Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics, 15, 773-774.
    • (1999) Bioinformatics , vol.15 , pp. 773-774
    • Kyrpides, N.C.1
  • 20
    • 18144453832 scopus 로고    scopus 로고
    • Errors in genome reviews
    • Kyrpides,N.C. and Ouzounis,C.A. (1998) Errors in genome reviews. Science, 281, 1457-1457.
    • (1998) Science , vol.281 , pp. 1457
    • Kyrpides, N.C.1    Ouzounis, C.A.2
  • 21
    • 0033042327 scopus 로고    scopus 로고
    • Whole-genome sequence annotation: 'Going wrong with confidence'
    • Kyrpides,N.C. and Ouzounis,C.A. (1999) Whole-genome sequence annotation: 'going wrong with confidence'. Mol. Microbiol., 32, 886-887.
    • (1999) Mol. Microbiol. , vol.32 , pp. 886-887
    • Kyrpides, N.C.1    Ouzounis, C.A.2
  • 22
    • 0030296854 scopus 로고    scopus 로고
    • KOW: A novel motif linking a bacterial transcription factor with ribosomal proteins
    • Kyrpides,N.C., Woese,C.R. and Ouzounis,C.A. (1996b) KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Trends Biochem Sci., 21, 425-426.
    • (1996) Trends Biochem. Sci. , vol.21 , pp. 425-426
    • Kyrpides, N.C.1    Woese, C.R.2    Ouzounis, C.A.3
  • 23
    • 0033598845 scopus 로고    scopus 로고
    • Isopentenyl diphosphate biosynthesis via a mevalonate-independent pathway: Isopentenyl monophosphate kinase catalyzes the terminal enzymatic step
    • Lange,B.M. and Croteau,R. (1999) Isopentenyl diphosphate biosynthesis via a mevalonate-independent pathway: isopentenyl monophosphate kinase catalyzes the terminal enzymatic step. Proc. Natl Acad. Sci. USA, 96, 13714-13719.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 13714-13719
    • Lange, B.M.1    Croteau, R.2
  • 24
    • 0030011428 scopus 로고    scopus 로고
    • Novelties from the complete genome of Mycoplasma genitalium
    • Ouzounis,C., Casari,G., Valencia,A. and Sander,C. (1996) Novelties from the complete genome of Mycoplasma genitalium. Mol. Microbiol., 20, 898-900.
    • (1996) Mol. Microbiol. , vol.20 , pp. 898-900
    • Ouzounis, C.1    Casari, G.2    Valencia, A.3    Sander, C.4
  • 25
    • 0027215805 scopus 로고
    • Homology of the NifS family of proteins to a new class of pyridoxal phosphate-dependent enzymes
    • Ouzounis,C. and Sander,C. (1993) Homology of the NifS family of proteins to a new class of pyridoxal phosphate-dependent enzymes. FEBS Lett., 322, 159-164.
    • (1993) FEBS Lett. , vol.322 , pp. 159-164
    • Ouzounis, C.1    Sander, C.2
  • 26
    • 0036175276 scopus 로고    scopus 로고
    • The future of genome-wide reannotation
    • comment2001.2001-2001.2006
    • Ouzounis,C.A. and Karp,P.D. (2002) The future of genome-wide reannotation. Genome Biol., comment2001.2001-2001.2006
    • (2002) Genome Biol.
    • Ouzounis, C.A.1    Karp, P.D.2
  • 27
    • 0033638015 scopus 로고    scopus 로고
    • CAST: An iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts
    • Promponas,V.J., Enright,A.J., Tsoka,S., Kreil,D.P., Leroy,C. et al. (2000) CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics, 16, 915-922.
    • (2000) Bioinformatics , vol.16 , pp. 915-922
    • Promponas, V.J.1    Enright, A.J.2    Tsoka, S.3    Kreil, D.P.4    Leroy, C.5
  • 28
    • 0031684427 scopus 로고    scopus 로고
    • Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm
    • Rigoutsos,I. and Floratos,A. (1998) Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics, 14, 55-67.
    • (1998) Bioinformatics , vol.14 , pp. 55-67
    • Rigoutsos, I.1    Floratos, A.2
  • 29
    • 0032719352 scopus 로고    scopus 로고
    • Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins
    • Rigoutsos,I., Floratos,A., Ouzounis,C., Gao,Y. and Parida,L. (1999) Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins. Proteins, 37, 264-277.
    • (1999) Proteins , vol.37 , pp. 264-277
    • Rigoutsos, I.1    Floratos, A.2    Ouzounis, C.3    Gao, Y.4    Parida, L.5
  • 30
    • 4243844882 scopus 로고    scopus 로고
    • Dictionary-driven protein annotation
    • IBM TJ Watson Research Center: #TR-RC22262
    • Rigoutsos,I., Huynh,T., Floratos,A., Parida,L. and Platt,D. (2001) Dictionary-driven protein annotation. IBM TJ Watson Research Center: #TR-RC22262.
    • (2001)
    • Rigoutsos, I.1    Huynh, T.2    Floratos, A.3    Parida, L.4    Platt, D.5
  • 32
    • 0031279916 scopus 로고    scopus 로고
    • The challenges of genome sequence annotation or 'the devil is in the details'
    • Smith,T.F. and Zhang,X. (1997) The challenges of genome sequence annotation or 'the devil is in the details'. Nat. Biotechnol., 15, 1222-1223.
    • (1997) Nat. Biotechnol. , vol.15 , pp. 1222-1223
    • Smith, T.F.1    Zhang, X.2
  • 33
    • 0032561496 scopus 로고    scopus 로고
    • Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis
    • Stephens,R.S., Kalman,S., Lammel,C., Fan,J., Marathe,R. et al. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science, 282, 754-759.
    • (1998) Science , vol.282 , pp. 754-759
    • Stephens, R.S.1    Kalman, S.2    Lammel, C.3    Fan, J.4    Marathe, R.5
  • 34
    • 0032544054 scopus 로고    scopus 로고
    • A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis
    • Takahashi,S., Kuzuyama,T., Watanabe,H. and Seto,H. (1998) A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis. Proc. Natl Acad. Sci. USA, 95, 9879-9884.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 9879-9884
    • Takahashi, S.1    Kuzuyama, T.2    Watanabe, H.3    Seto, H.4
  • 35
    • 0028802364 scopus 로고
    • Human diadenosine 5'′,5‴-P1,P4-tetraphosphate pyrophosphohydrolase is a member of the MutT family of nucleotide pyrophosphatases
    • Thorne,N.M., Hankin,S., Wilkinson,M.C., Nunez,C., Barraclough,R. et al. (1995) Human diadenosine 5'′,5‴-P1,P4-tetraphosphate pyrophosphohydrolase is a member of the MutT family of nucleotide pyrophosphatases. Biochem. J., 311, 717-721.
    • (1995) Biochem. J. , vol.311 , pp. 717-721
    • Thorne, N.M.1    Hankin, S.2    Wilkinson, M.C.3    Nunez, C.4    Barraclough, R.5
  • 36
    • 0033057344 scopus 로고    scopus 로고
    • Reproducibility in genome sequence annotation: The Plasmodium falciparum chromosome 2 case
    • Tsoka,S., Promponas,V. and Ouzounis,C.A. (1999) Reproducibility in genome sequence annotation: the Plasmodium falciparum chromosome 2 case. FEBS Lett., 451, 354-355.
    • (1999) FEBS Lett. , vol.451 , pp. 354-355
    • Tsoka, S.1    Promponas, V.2    Ouzounis, C.A.3
  • 37
    • 0032606076 scopus 로고    scopus 로고
    • Some measures of comparative performance in the three CASPs
    • Venclovas,C., Zemla,A., Fidelis,K. and Moult,J. (1999) Some measures of comparative performance in the three CASPs. Proteins, (suppl.), 231-237.
    • (1999) Proteins , Issue.SUPPL. , pp. 231-237
    • Venclovas, C.1    Zemla, A.2    Fidelis, K.3    Moult, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.