-
1
-
-
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
-
2
-
-
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
-
3
-
-
9144257886
-
The Pfam protein families database
-
Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32: D138-D141.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhammer, E.L.10
-
4
-
-
84957010453
-
The algorithmic of gene teams
-
Bergeron, A., Corteel, S., and Raffinot, M. 2002. The algorithmic of gene teams. Lecture Notes Comput. Sci. 2452: 464-476.
-
(2002)
Lecture Notes Comput. Sci.
, vol.2452
, pp. 464-476
-
-
Bergeron, A.1
Corteel, S.2
Raffinot, M.3
-
5
-
-
1042276327
-
Fast identification and statistical evaluation of segmental homologies in comparative maps
-
Calabrese, P.P., Chakravarty, S., and Vision, T.J. 2003. Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 19: i74-i80.
-
(2003)
Bioinformatics
, vol.19
-
-
Calabrese, P.P.1
Chakravarty, S.2
Vision, T.J.3
-
6
-
-
0242606435
-
Tests for gene clustering
-
Durand, D. and Sankoff, D. 2003. Tests for gene clustering. J. Comput. Biol. 10: 453-482.
-
(2003)
J. Comput. Biol.
, vol.10
, pp. 453-482
-
-
Durand, D.1
Sankoff, D.2
-
7
-
-
0031743421
-
Profile hidden Markov models
-
Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
8
-
-
0035753236
-
Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions
-
research0034.1-0034.7
-
Enright, A.J. and Ouzounis, C.A. 2001. Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol. 2: research0034.1-0034.7.
-
(2001)
Genome Biol.
, vol.2
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
9
-
-
0033523989
-
Protein interaction maps for complete genomes based on gene fusion events
-
Enright, A.J., Iliopoulos, I., Kyrpides, N.C., and Ouzounis, C.A. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90.
-
(1999)
Nature
, vol.402
, pp. 86-90
-
-
Enright, A.J.1
Iliopoulos, I.2
Kyrpides, N.C.3
Ouzounis, C.A.4
-
10
-
-
0034667776
-
A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters
-
Fujibuchi, W., Ogata, H., Matsuda, H., and Kanehisa, M. 2000. A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res. 28: 4021-4028.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4021-4028
-
-
Fujibuchi, W.1
Ogata, H.2
Matsuda, H.3
Kanehisa, M.4
-
11
-
-
0033561022
-
Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae
-
Fukuda, Y., Washio, T. and Tomita, M. 1999. Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. Nucleic Acids Res. 27: 1847-1853.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 1847-1853
-
-
Fukuda, Y.1
Washio, T.2
Tomita, M.3
-
12
-
-
0034084865
-
Who's your neighbor? New computational approaches for functional genomics
-
Galperin, M.Y. and Koonin, E.V. 2000. Who's your neighbor? New computational approaches for functional genomics. Nat. Biotech. 18: 609-613.
-
(2000)
Nat. Biotech.
, vol.18
, pp. 609-613
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
14
-
-
0023375315
-
Profile analysis: Detection of distantly related proteins
-
Gribskov, M., McLachlan, A.D., and Eisenberg, D. 1987. Profile analysis: Detection of distantly related proteins. Proc. Natl. Acad. Sci. 84: 4355-4358.
-
(1987)
Proc. Natl. Acad. Sci.
, vol.84
, pp. 4355-4358
-
-
Gribskov, M.1
McLachlan, A.D.2
Eisenberg, D.3
-
15
-
-
2942513067
-
A hybrid clustering approach to recognition of protein families in 114 microbial genomes
-
Harlow, T.J., Gogarten, J.P., and Ragan, M.A. 2004. A hybrid clustering approach to recognition of protein families in 114 microbial genomes. BMC Bioinformatics 5: 45.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 45
-
-
Harlow, T.J.1
Gogarten, J.P.2
Ragan, M.A.3
-
17
-
-
7244259101
-
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
-
Jaillon, O., Aury, J-M., Brunet, F., Petit, J-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957.
-
(2004)
Nature
, vol.431
, pp. 946-957
-
-
Jaillon, O.1
Aury, J.-M.2
Brunet, F.3
Petit, J.-L.4
Stange-Thomann, N.5
Mauceli, E.6
Bouneau, L.7
Fischer, C.8
Ozouf-Costaz, C.9
Bernot, A.10
-
18
-
-
0002650761
-
Cytoplasmic membrane
-
eds. F.C. Neidhardt et al., ASM Press, Washington, DC
-
Kadner, R.J. 1996. Cytoplasmic membrane. In Escherichia coli and Salmonella typhimurium, cellular and molecular biology (eds. F.C. Neidhardt et al.), pp. 58-87. ASM Press, Washington, DC.
-
(1996)
Escherichia Coli and Salmonella Typhimurium, Cellular and Molecular Biology
, pp. 58-87
-
-
Kadner, R.J.1
-
19
-
-
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-D280.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
20
-
-
0034625235
-
The impact of comparative genomics on our understanding of evolution
-
Koonin, E.V., Arawind, L., and Kondrashov, A.S. 2000. The impact of comparative genomics on our understanding of evolution. Cell 101: 573-576.
-
(2000)
Cell
, vol.101
, pp. 573-576
-
-
Koonin, E.V.1
Arawind, L.2
Kondrashov, A.S.3
-
21
-
-
3042703044
-
Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs
-
Korbel, J.O., Jensen, L.J., von Mering, C., and Bork, P. 2004. Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat. Biotech. 22: 911-917.
-
(2004)
Nat. Biotech.
, vol.22
, pp. 911-917
-
-
Korbel, J.O.1
Jensen, L.J.2
Von Mering, C.3
Bork, P.4
-
22
-
-
0042423438
-
Gene teams: A new formalization of gene clusters for comparative genomics
-
Luc, N., Risler, J-L., Bergeron, A., and Raffinot, M. 2003. Gene teams: A new formalization of gene clusters for comparative genomics. Comput. Biol. Chem. 27: 59-67.
-
(2003)
Comput. Biol. Chem.
, vol.27
, pp. 59-67
-
-
Luc, N.1
Risler, J.-L.2
Bergeron, A.3
Raffinot, M.4
-
23
-
-
0033523854
-
A combined algorithm for genome-wide prediction of protein function
-
Marcotte, E.M., Pellegrini, M., Thompson, M.J., Yeates, T.O., and Eisenberg, D. 1999a. A combined algorithm for genome-wide prediction of protein function. Nature 402: 83-86.
-
(1999)
Nature
, vol.402
, pp. 83-86
-
-
Marcotte, E.M.1
Pellegrini, M.2
Thompson, M.J.3
Yeates, T.O.4
Eisenberg, D.5
-
24
-
-
0033618555
-
Detecting protein function and protein-protein interactions from genome sequences
-
Marcotte, E.M., Pellegrini, M., Ho-Leung, N., Rice, D.W., Yeates, T.O., and Eisenberg, D. 1999b. Detecting protein function and protein-protein interactions from genome sequences. Science 30: 751-753.
-
(1999)
Science
, vol.30
, pp. 751-753
-
-
Marcotte, E.M.1
Pellegrini, M.2
Ho-Leung, N.3
Rice, D.W.4
Yeates, T.O.5
Eisenberg, D.6
-
25
-
-
16344381315
-
Statistical analysis of domains in interacting protein pairs
-
Nye, T.M., Berzuini, C., Gilks, W.R., Babu, M.M., and Teichmann, S.A. 2004. Statistical analysis of domains in interacting protein pairs. Bioinformatics 21: 993-1001.
-
(2004)
Bioinformatics
, vol.21
, pp. 993-1001
-
-
Nye, T.M.1
Berzuini, C.2
Gilks, W.R.3
Babu, M.M.4
Teichmann, S.A.5
-
26
-
-
0037190182
-
Fine mapping in tomato using microsynteny with the Arabidopsis genome: The Diageotropica (Dgt) locus
-
research0049.1-0049.11
-
Oh, K.C., Hardeman, C., Ivanchenko, M.G., Ellard-Ivet, M., Nebenfür, A., White, T.J., and Lomax, T.L. 2002. Fine mapping in tomato using microsynteny with the Arabidopsis genome: The Diageotropica (Dgt) locus. Genome Biol. 3: research0049.1-0049.11.
-
(2002)
Genome Biol.
, vol.3
-
-
Oh, K.C.1
Hardeman, C.2
Ivanchenko, M.G.3
Ellard-Ivet, M.4
Nebenfür, A.5
White, T.J.6
Lomax, T.L.7
-
27
-
-
0033055062
-
The use of gene clusters to infer functional coupling
-
Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D., and Maltsev, N. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. 96: 2896-2901.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 2896-2901
-
-
Overbeek, R.1
Fonstein, M.2
D'Souza, M.3
Pusch, G.D.4
Maltsev, N.5
-
28
-
-
0032751821
-
Incorrect use of the term synteny
-
Passarge, E., Horsthemke, B., and Farber, R.A. 1999. Incorrect use of the term synteny. Nat. Genet. 23: 387.
-
(1999)
Nat. Genet.
, vol.23
, pp. 387
-
-
Passarge, E.1
Horsthemke, B.2
Farber, R.A.3
-
29
-
-
0038306145
-
Modular assembly of genes and the evolution of new functions
-
Patthy, L. 2003. Modular assembly of genes and the evolution of new functions. Genetica 118: 217-231.
-
(2003)
Genetica
, vol.118
, pp. 217-231
-
-
Patthy, L.1
-
30
-
-
0037264074
-
Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
-
Pevzner, P. and Tesler, G. 2003. Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes. Genome Res. 13: 37-45.
-
(2003)
Genome Res.
, vol.13
, pp. 37-45
-
-
Pevzner, P.1
Tesler, G.2
-
31
-
-
9144270496
-
RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
-
Salgado, H., Gama-Castro, S., Martinez-Antonio, A., Diaz-Peredo, E., Sanchez-Solano, F., Peralta-Gil, M., Garcia-Alonso, D., Jimenez-Jacinto, V., Santos-Zavaleta, A., Bonavides-Martinez, C., et al. 2004. RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res. 32: D303-D306.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Salgado, H.1
Gama-Castro, S.2
Martinez-Antonio, A.3
Diaz-Peredo, E.4
Sanchez-Solano, F.5
Peralta-Gil, M.6
Garcia-Alonso, D.7
Jimenez-Jacinto, V.8
Santos-Zavaleta, A.9
Bonavides-Martinez, C.10
-
32
-
-
0038419681
-
Functional links between proteins
-
Sali, A. 1999. Functional links between proteins. Nature 402: 23-26.
-
(1999)
Nature
, vol.402
, pp. 23-26
-
-
Sali, A.1
-
33
-
-
0345447448
-
Rearrangements and genome evolution
-
Sankoff, D. 2003. Rearrangements and genome evolution. Curr. Opin. Gen. Dev. 13: 583-587.
-
(2003)
Curr. Opin. Gen. Dev.
, vol.13
, pp. 583-587
-
-
Sankoff, D.1
-
34
-
-
0346494857
-
FusionDB: A database for in-depth analysis of prokaryotic gene fusion events
-
Suhre, K. and Claverie, J-M. 2004. FusionDB: A database for in-depth analysis of prokaryotic gene fusion events. Nucleic Acids Res. 32: D273-D276.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Suhre, K.1
Claverie, J.-M.2
-
35
-
-
0035058359
-
Evolution of prokaryotic gene order: Genome rearrangements in closely related species
-
Suyama, M. and Bork, P. 2001. Evolution of prokaryotic gene order: Genome rearrangements in closely related species. Trends Genet. 17: 10-13.
-
(2001)
Trends Genet.
, vol.17
, pp. 10-13
-
-
Suyama, M.1
Bork, P.2
-
36
-
-
0010414313
-
Evolution of gene order conservation in prokaryotes
-
Tamames, J. 2001. Evolution of gene order conservation in prokaryotes. Genome Biol. 2: 0020.1-0020.11.
-
(2001)
Genome Biol.
, vol.2
-
-
Tamames, J.1
-
37
-
-
0345225320
-
Scaling up accurate phylogenetic reconstruction from gene-order data
-
Tang, J. and Moret, B.M. 2003. Scaling up accurate phylogenetic reconstruction from gene-order data. Bioinformatics 19: i305-i312.
-
(2003)
Bioinformatics
, vol.19
-
-
Tang, J.1
Moret, B.M.2
-
38
-
-
1842861592
-
Structure, function and evolution of multidomains proteins
-
Vogel, C., Bashton, M., Kerrison, N.D., Chothia, C., and Teichmann, S.A. 2004. Structure, function and evolution of multidomains proteins. Curr. Opin. Struct. Biol. 14: 208-216.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 208-216
-
-
Vogel, C.1
Bashton, M.2
Kerrison, N.D.3
Chothia, C.4
Teichmann, S.A.5
-
39
-
-
0037250152
-
STRING: A database of predicted functional associations between proteins
-
von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., and Snel, B. 2003. STRING: A database of predicted functional associations between proteins. Nucleic Acids Res. 31: 258-261.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 258-261
-
-
Von Mering, C.1
Huynen, M.2
Jaeggi, D.3
Schmidt, S.4
Bork, P.5
Snel, B.6
-
40
-
-
0034940467
-
Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes
-
Yanai, I., Derti, A., and DeLisi, C. 2001. Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes. Proc. Natl. Acad. Sci. 98: 7940-7945.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 7940-7945
-
-
Yanai, I.1
Derti, A.2
DeLisi, C.3
-
41
-
-
0036046771
-
Evolution of gene fusions: Horizontal transfer versus independent events
-
research0024.1-0024.13
-
Yanai, I., Wolf, Y.I., and Koonin, E.V. 2002. Evolution of gene fusions: Horizontal transfer versus independent events. Genome Biol. 3: research0024.1-0024.13.
-
(2002)
Genome Biol.
, vol.3
-
-
Yanai, I.1
Wolf, Y.I.2
Koonin, E.V.3
-
42
-
-
0032726692
-
Protomap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space
-
Yona, G., Linial, N., and Linial, M. 1999. Protomap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins 37: 360-378.
-
(1999)
Proteins
, vol.37
, pp. 360-378
-
-
Yona, G.1
Linial, N.2
Linial, M.3
-
43
-
-
32744458558
-
-
The directory of the Pfam ftp server that contains the Pfam annotations of the proteins in UniProt
-
ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database-files; The directory of the Pfam ftp server that contains the Pfam annotations of the proteins in UniProt.
-
-
-
-
44
-
-
32744466882
-
-
HMMER series of programs
-
http://hmmer.wustl.edu/; HMMER series of programs.
-
-
-
-
45
-
-
32744471936
-
-
The proteome Home Page at EBI
-
http://www.ebi.ac.uk/integr8/EBI-Integr8-HomePage.do; The proteome Home Page at EBI.
-
-
-
-
46
-
-
32744472676
-
-
DomainTeams full results and code downloads
-
http://lgi.infobiogen.fr/DomainTeams; DomainTeams full results and code downloads.
-
-
-
|