메뉴 건너뛰기




Volumn 34, Issue 1, 2006, Pages 53-65

MaGe: A microbial genome annotation system supported by synteny results

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ACINETOBACTER; ARTICLE; AUTOMATION; BACILLUS; BACTERIAL GENOME; BIOINFORMATICS; COMPUTER INTERFACE; FRANKIA; GENE FUNCTION; GENETIC DATABASE; GENETIC MODEL; INFORMATION PROCESSING; NEISSERIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PSEUDOALTEROMONAS; SYNTENY; YERSINIA;

EID: 31644444476     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkj406     Document Type: Article
Times cited : (314)

References (67)
  • 1
    • 0032229196 scopus 로고    scopus 로고
    • Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
    • Galperin,M.Y. and Koonin,E.V. (1998) Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol., 1, 55-67.
    • (1998) Silico Biol. , vol.1 , pp. 55-67
    • Galperin, M.Y.1    Koonin, E.V.2
  • 2
    • 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
  • 5
    • 0030052411 scopus 로고    scopus 로고
    • MAGPIE: Automated genome interpretation
    • Gaasterland,T. and Sensen,C.W. (1996) MAGPIE: Automated genome interpretation. Trends Genet., 12, 76-78.
    • (1996) Trends Genet. , vol.12 , pp. 76-78
    • Gaasterland, T.1    Sensen, C.W.2
  • 8
    • 0142119484 scopus 로고    scopus 로고
    • Viewing and annotating sequence data with Artemis
    • Berriman,M. and Rutherford,K. (2003) Viewing and annotating sequence data with Artemis. Brief Bioinform., 4, 124-132.
    • (2003) Brief Bioinform. , vol.4 , pp. 124-132
    • Berriman, M.1    Rutherford, K.2
  • 12
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: A fingerprint of proteins that physically interact
    • Dandekar,T., Snel,B., Huynen,M. and Bork,P. (1998) Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-328.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 13
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein protein interactions from genome sequences
    • Marcotte,E.M., Pellegrini,M., Ng,H.L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Detecting protein function and protein protein interactions from genome sequences. Science, 285, 751-753.
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 14
    • 0033301555 scopus 로고    scopus 로고
    • Use of contiguity on the chromosome to predict functional coupling
    • Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol., 1, 93-108.
    • (1999) Silico Biol. , vol.1 , pp. 93-108
    • Overbeek, R.1    Fonstein, M.2    D'Souza, M.3    Pusch, G.D.4    Maltsev, N.5
  • 16
    • 13444309602 scopus 로고    scopus 로고
    • Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
    • Doerks,T., von Mering,C. and Bork,P. (2004) Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucleic Acids Res., 32, 6321-6326.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6321-6326
    • Doerks, T.1    von Mering, C.2    Bork, P.3
  • 21
    • 0036137327 scopus 로고    scopus 로고
    • A probabilistic method for identifying start codons in bacterial genomes
    • Suzek,B.E., Ermolaeva,M.D., Schreiber,M. and Salzberg,S.L. (2001) A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics, 17, 1123-1130.
    • (2001) Bioinformatics , vol.17 , pp. 1123-1130
    • Suzek, B.E.1    Ermolaeva, M.D.2    Schreiber, M.3    Salzberg, S.L.4
  • 22
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 24
    • 0025663103 scopus 로고
    • Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures
    • d'Aubenton Carafa,Y., Brody,E. and Thermes,C. (1990) Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol., 216, 835-858.
    • (1990) J. Mol. Biol. , vol.216 , pp. 835-858
    • d'Aubenton Carafa, Y.1    Brody, E.2    Thermes, C.3
  • 25
    • 0033867676 scopus 로고    scopus 로고
    • Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: A possible model for their origin
    • Achaz,G., Coissac,E., Viari,A. and Netter,P. (2000) Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: A possible model for their origin. Mol. Biol. Evol., 17, 1268-1275.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1268-1275
    • Achaz, G.1    Coissac, E.2    Viari, A.3    Netter, P.4
  • 29
    • 0034530835 scopus 로고    scopus 로고
    • Using the COG database to improve gene recognition in complete genomes
    • Natale,D.A., Galperin,M.Y., Tatusov,R.L. and Koonin,E.V. (2000) Using the COG database to improve gene recognition in complete genomes. Genetica, 108, 9-17.
    • (2000) Genetica , vol.108 , pp. 9-17
    • Natale, D.A.1    Galperin, M.Y.2    Tatusov, R.L.3    Koonin, E.V.4
  • 32
    • 0035910270 scopus 로고    scopus 로고
    • Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
    • Krogh,A., Larsson,B., von Heijne,G. and Sonnhammer,E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
    • (2001) J. Mol. Biol. , vol.305 , pp. 567-580
    • Krogh, A.1    Larsson, B.2    von Heijne, G.3    Sonnhammer, E.L.4
  • 34
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough,J., Karplus,K., Hughey,R. and Chothia,C. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol., 313, 903-919.
    • (2001) J. Mol. Biol. , vol.313 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 36
    • 19544363942 scopus 로고    scopus 로고
    • Universal biases in protein composition of model prokaryotes
    • Pascal,G., Medigue,C. and Danchin,A. (2005) Universal biases in protein composition of model prokaryotes. Proteins, 60, 27-35.
    • (2005) Proteins , vol.60 , pp. 27-35
    • Pascal, G.1    Medigue, C.2    Danchin, A.3
  • 38
    • 18244386245 scopus 로고    scopus 로고
    • Nebulon: A system for the inference of functional relationships of gene products from the rearrangement of predicted operons
    • Janga,S.C., Collado-Vides,J. and Moreno-Hagelsieb,G. (2005) Nebulon: A system for the inference of functional relationships of gene products from the rearrangement of predicted operons. Nucleic Acids Res., 33, 2521-2530.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2521-2530
    • Janga, S.C.1    Collado-Vides, J.2    Moreno-Hagelsieb, G.3
  • 39
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 40
    • 28444453303 scopus 로고    scopus 로고
    • Syntons, metabolons and interactons: An exact graph-theoretical approach for exploring neighbourhood between genomic and functional data
    • Boyer,F., Morgat,A., Labarre,L., Pothier,J. and Viari,A. (2005) Syntons, metabolons and interactons: An exact graph-theoretical approach for exploring neighbourhood between genomic and functional data. Bioinformatics, 21, 4209-4215.
    • (2005) Bioinformatics , vol.21 , pp. 4209-4215
    • Boyer, F.1    Morgat, A.2    Labarre, L.3    Pothier, J.4    Viari, A.5
  • 41
    • 13444306641 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2005) NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.
    • (2005) Nucleic Acids Res. , vol.33
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 43
    • 27644434408 scopus 로고    scopus 로고
    • Phydbac 'Gene Function Predictor': A gene annotation tool based on genomic context analysis
    • Enault,F., Suhre,K. and Claverie,J.M. (2005) Phydbac 'Gene Function Predictor': A gene annotation tool based on genomic context analysis. BMC Bioinformatics, 6, 247.
    • (2005) BMC Bioinformatics , vol.6 , pp. 247
    • Enault, F.1    Suhre, K.2    Claverie, J.M.3
  • 46
    • 11244328060 scopus 로고    scopus 로고
    • The Pathway Tools software
    • Karp,P.D., Paley,S. and Romero,P. (2002) The Pathway Tools software. Bioinformatics, 18 (Suppl. 1), S225-S232.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Karp, P.D.1    Paley, S.2    Romero, P.3
  • 49
    • 13244268322 scopus 로고    scopus 로고
    • A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    • Green,M.L. and Karp,P.D. (2004) A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics, 5, 76.
    • (2004) BMC Bioinformatics , vol.5 , pp. 76
    • Green, M.L.1    Karp, P.D.2
  • 50
    • 16344376028 scopus 로고    scopus 로고
    • Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
    • Rahman,S.A., Advani,P., Schunk,R., Schrader,R. and Schomburg,D. (2005) Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics, 21, 1189-1193.
    • (2005) Bioinformatics , vol.21 , pp. 1189-1193
    • Rahman, S.A.1    Advani, P.2    Schunk, R.3    Schrader, R.4    Schomburg, D.5
  • 51
    • 23044485115 scopus 로고    scopus 로고
    • Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers
    • Green,M.L. and Karp,P.D. (2005) Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers. Nucleic Acids Res., 33, 4035-4039.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 4035-4039
    • Green, M.L.1    Karp, P.D.2
  • 53
    • 0347125234 scopus 로고    scopus 로고
    • GenProtEC: An updated and improved analysis of functions of Escherichia coli K-12 proteins
    • Serres,M.H., Goswami,S. and Riley,M. (2004) GenProtEC: An updated and improved analysis of functions of Escherichia coli K-12 proteins. Nucleic Acids Res., 32, D300-D302.
    • (2004) Nucleic Acids Res. , vol.32
    • Serres, M.H.1    Goswami, S.2    Riley, M.3
  • 54
    • 0033971754 scopus 로고    scopus 로고
    • EcoGene: A genome sequence database for Escherichia coli K-12
    • Rudd,K.E. (2000) EcoGene: A genome sequence database for Escherichia coli K-12. Nucleic Acids Res., 28, 60-64.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 60-64
    • Rudd, K.E.1
  • 57
    • 0034570532 scopus 로고    scopus 로고
    • MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products
    • Serres,M.H. and Riley,M. (2000) MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb. Comp. Genomics, 5, 205-222.
    • (2000) Microb. Comp. Genomics , vol.5 , pp. 205-222
    • Serres, M.H.1    Riley, M.2
  • 58
  • 60
    • 0030271920 scopus 로고    scopus 로고
    • Go hunting in sequence databases but watch out for the traps
    • Bork,P. and Bairoch,A. (1996) Go hunting in sequence databases but watch out for the traps. Trends Genet., 12, 425-427.
    • (1996) Trends Genet. , vol.12 , pp. 425-427
    • Bork, P.1    Bairoch, A.2
  • 61
    • 0036789272 scopus 로고    scopus 로고
    • Molecular evolution of the lysine biosynthetic pathways
    • Velasco,A.M., Leguina,J.I. and Lazcano,A. (2002) Molecular evolution of the lysine biosynthetic pathways. J. Mol. Evol., 55, 445-459.
    • (2002) J. Mol. Evol. , vol.55 , pp. 445-459
    • Velasco, A.M.1    Leguina, J.I.2    Lazcano, A.3
  • 62
    • 0033537677 scopus 로고    scopus 로고
    • The dual biosynthetic capability of N-acetylomithine aminotransferase in arginine and lysine biosynthesis
    • Ledwidge,R. and Blanchard,J.S. (1999) The dual biosynthetic capability of N-acetylomithine aminotransferase in arginine and lysine biosynthesis. Biochemistry, 38, 3019-3024.
    • (1999) Biochemistry , vol.38 , pp. 3019-3024
    • Ledwidge, R.1    Blanchard, J.S.2
  • 63
    • 0042431971 scopus 로고    scopus 로고
    • Identification and characterization of the last two unknown genes, dapC and dapF, in the succinylase branch of the L-lysine biosynthesis of Corynebacterium glutamicum
    • Hartmann,M., Tauch,A., Eggeling,L., Bathe,B., Mockel,B., Puhler,A. and Kalinowski,J. (2003) Identification and characterization of the last two unknown genes, dapC and dapF, in the succinylase branch of the L-lysine biosynthesis of Corynebacterium glutamicum. J. Biotechnol., 104, 199-211.
    • (2003) J. Biotechnol. , vol.104 , pp. 199-211
    • Hartmann, M.1    Tauch, A.2    Eggeling, L.3    Bathe, B.4    Mockel, B.5    Puhler, A.6    Kalinowski, J.7
  • 64
    • 0034044066 scopus 로고    scopus 로고
    • Characterization of a Bordetella pertussis diaminopimelate (DAP) biosynthesis locus identifies dapC, a novel gene coding for an N-succinyl-L, L-DAP aminotransferase
    • Fuchs,T.M., Schneider,B., Krumbach,K., Eggeling,L. and Gross,R. (2000) Characterization of a Bordetella pertussis diaminopimelate (DAP) biosynthesis locus identifies dapC, a novel gene coding for an N-succinyl-L,L-DAP aminotransferase. J. Bacteriol., 182, 3626-3631.
    • (2000) J. Bacteriol. , vol.182 , pp. 3626-3631
    • Fuchs, T.M.1    Schneider, B.2    Krumbach, K.3    Eggeling, L.4    Gross, R.5
  • 65
    • 0037057376 scopus 로고    scopus 로고
    • Genomic functional annotation using co-evolution profiles of gene clusters
    • RESEARCH0060
    • Zheng,Y., Roberts,R.J. and Kasif,S. (2002) Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol., 3, RESEARCH0060.
    • (2002) Genome Biol. , vol.3
    • Zheng, Y.1    Roberts, R.J.2    Kasif, S.3
  • 66
    • 0030929643 scopus 로고    scopus 로고
    • LASSAP, a LArge Scale Sequence compArison Package
    • Glemet,E. and Codani,J.J. (1997) LASSAP, a LArge Scale Sequence compArison Package. Comput. Appl. Biosci., 13, 137-143.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 137-143
    • Glemet, E.1    Codani, J.J.2
  • 67
    • 31644451485 scopus 로고    scopus 로고
    • GenoLink: Discovering drug target proteins by exploring networks of heterogeneous biological data
    • Durand,P., Labarre,L., Meil,A. and Wojcik,J. (2005) GenoLink: discovering drug target proteins by exploring networks of heterogeneous biological data. ERCIM, 60, 31-32.
    • (2005) ERCIM , vol.60 , pp. 31-32
    • Durand, P.1    Labarre, L.2    Meil, A.3    Wojcik, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.