-
1
-
-
0032229196
-
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
-
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
-
3
-
-
23144467676
-
BASys: A web server for automated bacterial genome annotation
-
Van Domselaar,G.H., Stothard,P., Shrivastava,S., Cruz,J.A., Guo,A., Dong,X., Lu,P., Szafron,D., Greiner,R. and Wishart,D.S. (2005) BASys: A web server for automated bacterial genome annotation. Nucleic Acids Res., 33, W455-W459.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Van Domselaar, G.H.1
Stothard, P.2
Shrivastava, S.3
Cruz, J.A.4
Guo, A.5
Dong, X.6
Lu, P.7
Szafron, D.8
Greiner, R.9
Wishart, D.S.10
-
4
-
-
13444283829
-
The PEDANT genome database in 2005
-
Riley,M.L., Schmidt,T., Wagner,C., Mewes,H.W. and Frishman,D. (2005) The PEDANT genome database in 2005. Nucleic Acids Res., 33, D308-D310.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Riley, M.L.1
Schmidt, T.2
Wagner, C.3
Mewes, H.W.4
Frishman, D.5
-
5
-
-
0030052411
-
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
-
6
-
-
0033958091
-
The GeneQuiz web server: Protein functional analysis through the Web
-
Hoersch,S., Leroy,C., Brown,N.P., Andrade,M.A. and Sander,C. (2000) The GeneQuiz web server: Protein functional analysis through the Web. Trends Biochem. Sci., 25, 33-35.
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 33-35
-
-
Hoersch, S.1
Leroy, C.2
Brown, N.P.3
Andrade, M.A.4
Sander, C.5
-
7
-
-
0037208159
-
The ERGO genome analysis and discovery system
-
Overbeek,R., Larsen,N., Walunas,T., D'Souza,M., Pusch,G., Selkov,E.,Jr, Liolios,K., Joukov,V., Kaznadzey,D., Anderson,I. et al. (2003) The ERGO genome analysis and discovery system. Nucleic Acids Res., 31, 164-171.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 164-171
-
-
Overbeek, R.1
Larsen, N.2
Walunas, T.3
D'Souza, M.4
Pusch, G.5
Selkov Jr., E.6
Liolios, K.7
Joukov, V.8
Kaznadzey, D.9
Anderson, I.10
-
8
-
-
0142119484
-
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
-
9
-
-
0037561991
-
GenDB - An open source genome annotation system for prokaryote genomes
-
Meyer,F., Goesmann,A., McHardy,A.C., Bartels,D., Bekel,T., Clausen,J., Kalinowski,J., Linke,B., Rupp,O., Giegerich,R. et al. (2003) GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res., 31, 2187-2195.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 2187-2195
-
-
Meyer, F.1
Goesmann, A.2
McHardy, A.C.3
Bartels, D.4
Bekel, T.5
Clausen, J.6
Kalinowski, J.7
Linke, B.8
Rupp, O.9
Giegerich, R.10
-
10
-
-
1842611886
-
CAAT-Box, contigs-assembly and annotation tool-box for genome sequencing projects
-
Frangeul,L., Glaser,P., Rusniok,C., Buchrieser,C., Duchaud,E., Dehoux,P. and Kunst,F. (2004) CAAT-Box, contigs-assembly and annotation tool-box for genome sequencing projects. Bioinformatics, 20, 790-797.
-
(2004)
Bioinformatics
, vol.20
, pp. 790-797
-
-
Frangeul, L.1
Glaser, P.2
Rusniok, C.3
Buchrieser, C.4
Duchaud, E.5
Dehoux, P.6
Kunst, F.7
-
11
-
-
8844261125
-
A System for Automated Bacterial (genome) Integrated Annotation - SABIA
-
Almeida,L.G., Paixao,R., Souza,R.C., Costa,G.C., Barrientos,F.J., Santos,M.T., Almeida,D.F. and Vasconcelos,A.T. (2004) A System for Automated Bacterial (genome) Integrated Annotation - SABIA. Bioinformatics, 20, 2832-2833.
-
(2004)
Bioinformatics
, vol.20
, pp. 2832-2833
-
-
Almeida, L.G.1
Paixao, R.2
Souza, R.C.3
Costa, G.C.4
Barrientos, F.J.5
Santos, M.T.6
Almeida, D.F.7
Vasconcelos, A.T.8
-
12
-
-
0032169271
-
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
-
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
-
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
-
15
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
16
-
-
13444309602
-
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
-
17
-
-
10244260491
-
Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium
-
Barbe,V., Vallenet,D., Fonknechten,N., Kreimeyer,A., Oztas,S., Labarre,L., Cruveiller,S., Robert,C., Duprat,S., Wincker,P. et al. (2004) Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Res., 32, 5766-5779.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5766-5779
-
-
Barbe, V.1
Vallenet, D.2
Fonknechten, N.3
Kreimeyer, A.4
Oztas, S.5
Labarre, L.6
Cruveiller, S.7
Robert, C.8
Duprat, S.9
Wincker, P.10
-
18
-
-
25844462537
-
Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
-
Medigue,C., Krin,E., Pascal,G., Barbe,V., Bernsel,A., Bertin,P.N., Cheung,F., Cruveiller,S., D'Amico,S., Duilio,A. et al. (2005) Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. Genome Res., 15, 1325-1335.
-
(2005)
Genome Res.
, vol.15
, pp. 1325-1335
-
-
Medigue, C.1
Krin, E.2
Pascal, G.3
Barbe, V.4
Bernsel, A.5
Bertin, P.N.6
Cheung, F.7
Cruveiller, S.8
D'Amico, S.9
Duilio, A.10
-
19
-
-
0043123003
-
AMIGene: Annotation of MIcrobial Genes
-
Bocs,S., Cruveiller,S., Vallenet,D., Nuel,G. and Medigue,C. (2003) AMIGene: Annotation of MIcrobial Genes. Nucleic Acids Res., 31, 3723-3726.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3723-3726
-
-
Bocs, S.1
Cruveiller, S.2
Vallenet, D.3
Nuel, G.4
Medigue, C.5
-
20
-
-
23144444587
-
MICheck: A web tool for fast checking of syntactic annotations of bacterial genomes
-
Cruveiller,S., Le Saux,J., Vallenet,D., Lajus,A., Bocs,S. and Medigue,C. (2005) MICheck: A web tool for fast checking of syntactic annotations of bacterial genomes. Nucleic Acids Res., 33, W471-W479.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Cruveiller, S.1
Le Saux, J.2
Vallenet, D.3
Lajus, A.4
Bocs, S.5
Medigue, C.6
-
21
-
-
0036137327
-
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
-
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
-
23
-
-
13444252847
-
Rfam: Annotating non-coding RNAs in complete genomes
-
Griffiths-Jones,S., Moxon,S., Marshall,M., Khanna,A., Eddy,S.R. and Bateman,A. (2005) Rfam: Annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, 13121-13124.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 13121-13124
-
-
Griffiths-Jones, S.1
Moxon, S.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
Bateman, A.6
-
24
-
-
0025663103
-
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
-
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
-
26
-
-
0030801002
-
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., Miller,W. and Lipman,D.J. (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
Miller, W.6
Lipman, D.J.7
-
27
-
-
13444273448
-
The Universal Protein Resource (UniProt)
-
Bairoch,A., Apweiler,R., Wu,C.H., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R., Magrane,M. et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res., 33, D154-D159.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Bairoch, A.1
Apweiler, R.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
Ferro, S.6
Gasteiger, E.7
Huang, H.8
Lopez, R.9
Magrane, M.10
-
28
-
-
13444282474
-
InterPro, progress and status in 2005
-
Mulder,N.J., Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Binns,D., Bradley,P., Bork,P., Bucher,P., Cerutti,L. et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res., 33, D201-D205.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Mulder, N.J.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Bradley, P.7
Bork, P.8
Bucher, P.9
Cerutti, L.10
-
29
-
-
0034530835
-
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
-
30
-
-
0345531106
-
Enzyme-specific profiles for genome annotation: PRIAM
-
Claudel-Renard,C., Chevalet,C., Faraut,T. and Kahn,D. (2003) Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res., 31, 6633-6639.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6633-6639
-
-
Claudel-Renard, C.1
Chevalet, C.2
Faraut, T.3
Kahn, D.4
-
31
-
-
0042423439
-
Automated annotation of microbial proteomes in SWISS-PROT
-
Gattiker,A., Michoud,K., Rivoire,C., Auchincloss,A.H., Coudert,E., Lima,T., Kersey,P., Pagni,M., Sigrist,C.J., Lachaize,C. et al. (2003) Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem., 27, 49-58.
-
(2003)
Comput. Biol. Chem.
, vol.27
, pp. 49-58
-
-
Gattiker, A.1
Michoud, K.2
Rivoire, C.3
Auchincloss, A.H.4
Coudert, E.5
Lima, T.6
Kersey, P.7
Pagni, M.8
Sigrist, C.J.9
Lachaize, C.10
-
32
-
-
0035910270
-
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
-
33
-
-
3042521098
-
Improved prediction of signal peptides: SignalP 3.0
-
Bendtsen,J.D., Nielsen,H., von Heijne,G. and Brunak,S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340, 783-795.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 783-795
-
-
Bendtsen, J.D.1
Nielsen, H.2
von Heijne, G.3
Brunak, S.4
-
34
-
-
0035798406
-
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
-
35
-
-
0346494941
-
SCOP database in 2004: Refinements integrate structure and sequence family data
-
Andreeva,A., Howorth,D., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2004) SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res., 32, D226-D229.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Andreeva, A.1
Howorth, D.2
Brenner, S.E.3
Hubbard, T.J.4
Chothia, C.5
Murzin, A.G.6
-
36
-
-
19544363942
-
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
-
37
-
-
13444249988
-
STRING: Known and predicted protein-protein associations, integrated and transferred across organisms
-
von Mering,C., Jensen,L.J., Snel,B., Hooper,S.D., Krupp,M., Foglierini,M., Jouffre,N., Huynen,M.A. and Bork,P. (2005) STRING: Known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res., 33, D433-D437.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
von Mering, C.1
Jensen, L.J.2
Snel, B.3
Hooper, S.D.4
Krupp, M.5
Foglierini, M.6
Jouffre, N.7
Huynen, M.A.8
Bork, P.9
-
38
-
-
18244386245
-
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
-
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
-
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
-
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
-
42
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek,R., Begley,T., Buder,R.M., Choudhuri,J.V., Chuang,H.Y., Cohoon,M., de Crecy-Lagard,V., Diaz,N., Disz,T., Edwards,R. et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res., 33, 5691-5702.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Buder, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
de Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
-
43
-
-
27644434408
-
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
-
44
-
-
0346801873
-
The Gene Ontology (GO) database and informatics resource
-
Harris,M.A., Clark,J., Ireland,A., Lomax,J., Ashburner,M., Foulger,R., Eilbeck,K., Lewis,S., Marshall,B., Mungall,C. et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258-D261.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Harris, M.A.1
Clark, J.2
Ireland, A.3
Lomax, J.4
Ashburner, M.5
Foulger, R.6
Eilbeck, K.7
Lewis, S.8
Marshall, B.9
Mungall, C.10
-
45
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
Kanehisa,M., Goto,S., Kawashima,S., Okuno,Y. and Hattori,M. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32, D277-280.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
46
-
-
11244328060
-
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
-
47
-
-
24044469030
-
Querying and computing with BioCyc databases
-
Krummenacker,M., Paley,S., Mueller,L., Yan,T. and Karp,P.D. (2005) Querying and computing with BioCyc databases. Bioinformatics, 21, 3454-3455.
-
(2005)
Bioinformatics
, vol.21
, pp. 3454-3455
-
-
Krummenacker, M.1
Paley, S.2
Mueller, L.3
Yan, T.4
Karp, P.D.5
-
48
-
-
0346494819
-
MetaCyc: A multiorganism database of metabolic pathways and enzymes
-
Krieger,C.J., Zhang,P., Mueller,L.A., Wang,A., Paley,S., Arnaud,M., Pick,J., Rhee,S.Y. and Karp,P.D. (2004) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res., 32, D438-D442.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Krieger, C.J.1
Zhang, P.2
Mueller, L.A.3
Wang, A.4
Paley, S.5
Arnaud, M.6
Pick, J.7
Rhee, S.Y.8
Karp, P.D.9
-
49
-
-
13244268322
-
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
-
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
-
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
-
52
-
-
13444304365
-
Integr8 and Genome Reviews: Integrated views of complete genomes and proteomes
-
Kersey,P., Bower,L., Morris,L., Horne,A., Petryszak,R., Kanz,C., Kanapin,A., Das,U., Michoud,K., Phan,I. et al. (2005) Integr8 and Genome Reviews: Integrated views of complete genomes and proteomes. Nucleic Acids Res., 33, D297-D302.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Kersey, P.1
Bower, L.2
Morris, L.3
Horne, A.4
Petryszak, R.5
Kanz, C.6
Kanapin, A.7
Das, U.8
Michoud, K.9
Phan, I.10
-
53
-
-
0347125234
-
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
-
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
-
55
-
-
13444302756
-
Pseudomonas aeruginosa Genome Database and PseudoCAP: Facilitating community-based, continually updated, genome annotation
-
Winsor,G.L., Lo,R., Sui,S.J., Ung,K.S., Huang,S., Cheng,D., Ching,W.K., Hancock,R.E. and Brinkman,F.S. (2005) Pseudomonas aeruginosa Genome Database and PseudoCAP: Facilitating community-based, continually updated, genome annotation. Nucleic Acids Res., 33, D338-D343.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Winsor, G.L.1
Lo, R.2
Sui, S.J.3
Ung, K.S.4
Huang, S.5
Cheng, D.6
Ching, W.K.7
Hancock, R.E.8
Brinkman, F.S.9
-
56
-
-
0036081063
-
SubtiList: The reference database for the Bacillus subtilis genome
-
Moszer,I., Jones,L.M., Moreira,S., Fabry,C. and Danchin,A. (2002) SubtiList: The reference database for the Bacillus subtilis genome. Nucleic Acids Res., 30, 62-65.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 62-65
-
-
Moszer, I.1
Jones, L.M.2
Moreira, S.3
Fabry, C.4
Danchin, A.5
-
57
-
-
0034570532
-
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
-
-
0037249633
-
The TIGRFAMs database of protein families
-
Haft,D.H., Selengut,J.D. and White,O. (2003) The TIGRFAMs database of protein families. Nucleic Acids Res., 31, 371-373.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 371-373
-
-
Haft, D.H.1
Selengut, J.D.2
White, O.3
-
59
-
-
9144257282
-
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
-
Ruepp,A., Zollner,A., Maier,D., Albermann,K., Hani,J., Mokrejs,M., Tetko,I., Guldener,U., Mannhaupt,G., Munsterkotter,M. et al. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res., 32, 5539-5545.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5539-5545
-
-
Ruepp, A.1
Zollner, A.2
Maier, D.3
Albermann, K.4
Hani, J.5
Mokrejs, M.6
Tetko, I.7
Guldener, U.8
Mannhaupt, G.9
Munsterkotter, M.10
-
60
-
-
0030271920
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|