-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, 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
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papado poulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papado Poulos, J.5
-
3
-
-
0036226603
-
BLAT - The BLAST-like alignment tool
-
Kent WJ (2002) BLAT - the BLAST-like alignment tool. Genome Res 12: 656-64.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
4
-
-
79952256999
-
Adaptive seeds tame genomic sequence comparison
-
Kie lbasa SM, Wan R, Sato K, Horton P, Frith MC (2011) Adaptive seeds tame genomic sequence comparison. Genome Res 21: 487-493.
-
(2011)
Genome Res
, vol.21
, pp. 487-493
-
-
Kielbasa, S.M.1
Wan, R.2
Sato, K.3
Horton, P.4
Frith, M.C.5
-
5
-
-
77957244650
-
Search and clustering orders of magnitude faster than blast
-
Edgar RC (2010) Search and clustering orders of magnitude faster than blast. Bioinformatics 26: 2460-1.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
6
-
-
0042902833
-
The cog database: An updated version includes eukaryotes
-
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The cog database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
-
7
-
-
33747892409
-
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
-
Alexeyenko A, Tamas I, Liu G, Sonnhammer EL (2006) Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22: e9-15.
-
(2006)
Bioinformatics
, vol.22
-
-
Alexeyenko, A.1
Tamas, I.2
Liu, G.3
Sonnhammer, E.L.4
-
8
-
-
33747817416
-
Roundup: A multi-genome repository of orthologs and evolutionary distances
-
DOI 10.1093/bioinformatics/btl286
-
Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, et al. (2006) Roundup: a multi-genome repository of orthologs and evolutionary distances. Bioinformatics 22: 2044-6. (Pubitemid 44283018)
-
(2006)
Bioinformatics
, vol.22
, Issue.16
, pp. 2044-2046
-
-
DeLuca, T.F.1
Wu, I.-H.2
Pu, J.3
Monaghan, T.4
Peshkin, L.5
Singh, S.6
Wall, D.P.7
-
9
-
-
84891757311
-
eggNOG v4.0: Nested orthology inference across 3686 organisms
-
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, et al. (2014) eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic acids research 42: D231-9.
-
(2014)
Nucleic Acids Research
, vol.42
-
-
Powell, S.1
Forslund, K.2
Szklarczyk, D.3
Trachana, K.4
Roth, A.5
-
10
-
-
84876517441
-
KEGG OC: A large-scale automatic construction of taxonomy-based ortholog clusters
-
Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, et al. (2013) KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic acids research 41: D353-7.
-
(2013)
Nucleic Acids Research
, vol.41
-
-
Nakaya, A.1
Katayama, T.2
Itoh, M.3
Hiranuka, K.4
Kawashima, S.5
-
11
-
-
84876590045
-
OrtholugeDB: A bacterial and archaeal orthology resource for improved comparative genomic analysis
-
Whiteside MD, Winsor GL, Laird MR, Brinkman FSL (2013) OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. Nucleic acids research 41: D366-76.
-
(2013)
Nucleic Acids Research
, vol.41
-
-
Whiteside, M.D.1
Winsor, G.L.2
Laird, M.R.3
Brinkman, F.S.L.4
-
12
-
-
84876566349
-
OrthoDB: A hierarchical catalog of animal, fungal and bacterial orthologs
-
Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV (2013) OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic acids research 41: D358-65.
-
(2013)
Nucleic Acids Research
, vol.41
-
-
Waterhouse, R.M.1
Tegenfeldt, F.2
Li, J.3
Zdobnov, E.M.4
Kriventseva, E.V.5
-
13
-
-
38849135019
-
Choosing BLAST options for better detection of orthologs as reciprocal best hits
-
DOI 10.1093/bioinformatics/btm585
-
Moreno-Hagelsieb G, Latimer K (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 24: 319-324. (Pubitemid 351189006)
-
(2008)
Bioinformatics
, vol.24
, Issue.3
, pp. 319-324
-
-
Moreno-Hagelsieb, G.1
Latimer, K.2
-
14
-
-
0033965854
-
NCBI's LocusLink and RefSeq
-
Maglott DR, Katz KS, Sicotte H, Pruitt KD (2000) NCBI's LocusLink and RefSeq. Nucleic Acids Res 28: 126-128. (Pubitemid 30047733)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 126-128
-
-
Maglott, D.R.1
Katz, K.S.2
Sicotte, H.3
Pruitt, K.D.4
-
15
-
-
84891822155
-
RefSeq microbial genomes database: New representation and annotation strategy
-
Tatusova T, Ciufo S, Fedorov B, O'Neill K, Tolstoy I (2014) RefSeq microbial genomes database: new representation and annotation strategy. Nucleic acids research 42: D553-9.
-
(2014)
Nucleic Acids Research
, vol.42
-
-
Tatusova, T.1
Ciufo, S.2
Fedorov, B.3
O'Neill, K.4
Tolstoy, I.5
-
16
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
DOI 10.1093/nar/gkg095
-
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31: 365-70. (Pubitemid 36157284)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.-C.4
Estreicher, A.5
Gasteiger, E.6
Martin, M.J.7
Michoud, K.8
O'Donovan, C.9
Phan, I.10
Pilbout, S.11
Schneider, M.12
-
17
-
-
0042423439
-
Automated annotation of microbial proteomes in SWISS-PROT
-
Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, 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
-
18
-
-
0035875343
-
GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
-
Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29: 2607-2618. (Pubitemid 32600318)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.12
, pp. 2607-2618
-
-
Besemer, J.1
Lomsadze, A.2
Borodovsky, M.3
-
19
-
-
40549120596
-
The RAST Server: Rapid annotations using subsystems technology
-
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
-
20
-
-
84873739550
-
Improving microbial genome annotations in an integrated database context
-
Chen IMA, Markowitz VM, Chu K, Anderson I, Mavromatis K, et al. (2013) Improving microbial genome annotations in an integrated database context. PLoS ONE 8: e54859.
-
(2013)
PLoS ONE
, vol.8
-
-
Chen, I.M.A.1
Markowitz, V.M.2
Chu, K.3
Anderson, I.4
Mavromatis, K.5
-
21
-
-
84891776599
-
PATRIC, the bacterial bioinformatics database and analysis resource
-
Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, et al. (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic acids research 42: D581-91.
-
(2014)
Nucleic Acids Research
, vol.42
-
-
Wattam, A.R.1
Abraham, D.2
Dalay, O.3
Disz, T.L.4
Driscoll, T.5
-
22
-
-
0034178257
-
Homology a personal view on some of the problems
-
Fitch WM (2000) Homology a personal view on some of the problems. Trends Genet 16: 227-231.
-
(2000)
Trends Genet
, vol.16
, pp. 227-231
-
-
Fitch, W.M.1
-
24
-
-
20044369186
-
An adaptive radiation model for the origin of new gene functions
-
Francino MP (2005) An adaptive radiation model for the origin of new gene functions. Nat Genet 37: 573-7.
-
(2005)
Nat Genet
, vol.37
, pp. 573-577
-
-
Francino, M.P.1
-
25
-
-
84863639111
-
Resolving the ortholog conjecture: Orthologs tend to be weakly, but significantly, more similar in function than paralogs
-
Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C (2012) Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Computational Biology 8: e1002514.
-
(2012)
PLoS Computational Biology
, vol.8
-
-
Altenhoff, A.M.1
Studer, R.A.2
Robinson-Rechavi, M.3
Dessimoz, C.4
-
26
-
-
84870655983
-
The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data
-
Chen X, Zhang J (2012) The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data. PLoS Computational Biology.
-
(2012)
PLoS Computational Biology
-
-
Chen, X.1
Zhang, J.2
-
27
-
-
84861123821
-
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report
-
Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA, et al. (2012) On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Computational Biology 8: e1002386.
-
(2012)
PLoS Computational Biology
, vol.8
-
-
Thomas, P.D.1
Wood, V.2
Mungall, C.J.3
Lewis, S.E.4
Blake, J.A.5
-
28
-
-
84876665869
-
Functional and evolutionary implications of gene orthology
-
Gabaldón T, Koonin EV (2013) Functional and evolutionary implications of gene orthology. Nature Reviews Genetics 14: 360-366.
-
(2013)
Nature Reviews Genetics
, vol.14
, pp. 360-366
-
-
Gabaldón, T.1
Koonin, E.V.2
-
29
-
-
6044261571
-
Conservation of adjacency as evidence of paralogous operons
-
DOI 10.1093/nar/gkh882
-
Janga SC, Moreno-Hagelsieb G (2004) Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res 32: 5392-7. (Pubitemid 39545656)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.18
, pp. 5392-5397
-
-
Janga, S.C.1
Moreno-Hagelsieb, G.2
-
30
-
-
38549163152
-
TreeFam: 2008 Update
-
DOI 10.1093/nar/gkm1005
-
Ruan J, Li H, Chen Z, Coghlan A, Coin LJM, et al. (2008) TreeFam: 2008 Update. Nucleic Acids Res 36: D735-40. (Pubitemid 351149816)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Ruan, J.1
Li, H.2
Chen, Z.3
Coghlan, A.4
Coin, L.J.M.5
Guo, Y.6
Heacute7
riche, J.-K.8
Hu, Y.9
Kristiansen, K.10
Li, R.11
Liu, T.12
Moses, A.13
Qin, J.14
Vang, S.15
Vilella, A.J.16
Ureta-Vidal, A.17
Bolund, L.18
Wang, J.19
Durbin, R.20
more..
-
31
-
-
59949096873
-
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
-
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, et al. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Research 19: 327-335.
-
(2009)
Genome Research
, vol.19
, pp. 327-335
-
-
Vilella, A.J.1
Severin, J.2
Ureta-Vidal, A.3
Heng, L.4
Durbin, R.5
-
32
-
-
84883588374
-
The PhyloFacts FAT-CAT web server: Ortholog identification and function prediction using fast approximate tree classification
-
Afrasiabi C, Samad B, Dineen D, Meacham C, Sjölander K (2013) The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. Nucleic Acids Res 41: W242-8.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Afrasiabi, C.1
Samad, B.2
Dineen, D.3
Meacham, C.4
Sjölander, K.5
-
33
-
-
0030660581
-
A genomic perspective on protein families
-
DOI 10.1126/science.278.5338.631
-
Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278: 631-637. (Pubitemid 27464953)
-
(1997)
Science
, vol.278
, Issue.5338
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
34
-
-
0032491377
-
Predicting function: From genes to genomes and back
-
DOI 10.1006/jmbi.1998.2144
-
Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, et al. (1998) Predicting function: from genes to genomes and back. J Mol Biol 283: 707-25. (Pubitemid 28495340)
-
(1998)
Journal of Molecular Biology
, vol.283
, Issue.4
, pp. 707-725
-
-
Bork, P.1
Dandekar, T.2
Diaz-Lazcoz, Y.3
Eisenhaber, F.4
Huynen, M.5
Yuan, Y.6
-
35
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith TF, Waterman MS (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
-
36
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-10.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
37
-
-
0025272240
-
Rapid and sensitive sequence comparison with fastp and fasta
-
Pearson WR (1990) Rapid and sensitive sequence comparison with fastp and fasta. Methods Enzymol 183: 63-98.
-
(1990)
Methods Enzymol
, vol.183
, pp. 63-98
-
-
Pearson, W.R.1
-
38
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1474.
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett III, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
-
39
-
-
0030731108
-
The complete genome sequence of the gram-positive bacterium Bacillus subtilis
-
DOI 10.1038/36786
-
Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, et al. (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249-256. (Pubitemid 27513299)
-
(1997)
Nature
, vol.390
, Issue.6657
, pp. 249-256
-
-
Kunst, F.1
Ogasawara, N.2
Moszer, I.3
Albertini, A.M.4
Alloni, G.5
Azevedo, V.6
Bertero, M.G.7
Bessieres, P.8
Bolotin, A.9
Borchert, S.10
Borriss, R.11
Boursier, L.12
Brans, A.13
Braun, M.14
Brignell, S.C.15
Bron, S.16
Brouillet, S.17
Bruschi, C.V.18
Caldwell, B.19
Capuano, V.20
Carter, N.M.21
Choi, S.-K.22
Codani, J.-J.23
Connerton, I.F.24
Cummings, N.J.25
Daniel, R.A.26
Denizot, F.27
Devine, K.M.28
Dusterhoft, A.29
Ehrlich, S.D.30
Emmerson, P.T.31
Entian, K.D.32
Errington, J.33
Fabret, C.34
Ferrari, E.35
Foulger, D.36
Fritz, C.37
Fujita, M.38
Fujita, Y.39
Fuma, S.40
Galizzi, A.41
Galleron, N.42
Ghim, S.-Y.43
Glaser, P.44
Goffeau, A.45
Golightly, E.J.46
Grandi, G.47
Guiseppi, G.48
Guy, B.J.49
Haga, K.50
Haiech, J.51
Harwood, C.R.52
Henaut, A.53
Hilbert, H.54
Holsappel, S.55
Hosono, S.56
Hullo, M.-F.57
Itaya, M.58
Jones, L.59
Joris, B.60
Karamata, D.61
Kasahara, Y.62
Klaerr-Blanchard, M.63
Klein, C.64
Kobayashi, Y.65
Koetter, P.66
Koningstein, G.67
Krogh, S.68
Kumano, M.69
Kurita, K.70
Lapidus, A.71
Lardinois, S.72
Lauber, J.73
Lazarevic, V.74
Lee, S.-M.75
Levine, A.76
Liu, H.77
Masuda, S.78
Mauel, C.79
Medigue, C.80
Medina, N.81
Mellado, R.P.82
Mizuno, M.83
Moestl, D.84
Nakai, S.85
Noback, M.86
Noone, D.87
O'Reilly, M.88
Ogawa, K.89
Ogiwara, A.90
Oudega, B.91
Park, S.-H.92
Parro, V.93
Pohl, T.M.94
Portetelle, D.95
Porwollik, S.96
Prescott, A.M.97
Presecan, E.98
Pujic, P.99
more..
-
40
-
-
0035988323
-
The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea
-
Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, et al. (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. Journal of molecular microbiology and biotechnology 4: 453-461. (Pubitemid 34784706)
-
(2002)
Journal of Molecular Microbiology and Biotechnology
, vol.4
, Issue.4
, pp. 453-461
-
-
Deppenmeier, U.1
Johann, A.2
Hartsch, T.3
Merkl, R.4
Schmitz, R.A.5
Martinez-Arias, R.6
Henne, A.7
Wiezer, A.8
Baumer, S.9
Jacobi, C.10
Bruggemann, H.11
Lienard, T.12
Christmann, A.13
Bomeke, M.14
Steckel, S.15
Bhattacharyya, A.16
Lykidis, A.17
Overbeek, R.18
Klenk, H.-P.19
Gunsalus, R.P.20
Fritz, H.-J.21
Gottschalk, G.22
more..
-
41
-
-
10244239321
-
Life with 6000 genes
-
DOI 10.1126/science.274.5287.546
-
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, et al. (1996) Life with 6000 genes. Science 274: 546-567. (Pubitemid 26360429)
-
(1996)
Science
, vol.274
, Issue.5287
, pp. 546-567
-
-
Goffeau, A.1
Barrell, G.2
Bussey, H.3
Davis, R.W.4
Dujon, B.5
Feldmann, H.6
Galibert, F.7
Hoheisel, J.D.8
Jacq, C.9
Johnston, M.10
Louis, E.J.11
Mewes, H.W.12
Murakami, Y.13
Philippsen, P.14
Tettelin, H.15
Oliver, S.G.16
-
42
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 29: 2994-3005. (Pubitemid 32685225)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.14
, pp. 2994-3005
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
43
-
-
27144489108
-
Protein database searches using compositionally adjusted substitution matrices
-
DOI 10.1111/j.1742-4658.2005.04945.x
-
Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, et al. (2005) Protein database searches using compositionally adjusted substitution matrices. The FEBS journal 272: 5101-5109. (Pubitemid 41503143)
-
(2005)
FEBS Journal
, vol.272
, Issue.20
, pp. 5101-5109
-
-
Altschul, S.F.1
Wootton, J.C.2
Gertz, E.M.3
Agarwala, R.4
Morgulis, A.5
Schaffer, A.A.6
Yu, Y.-K.7
-
44
-
-
33846659488
-
Composition-based statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST
-
Gertz EM, Yu YK, Agarwala R, Schäffer AA, Altschul SF (2006) Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC biology 4: 41.
-
(2006)
BMC Biology
, vol.4
, pp. 41
-
-
Gertz, E.M.1
Yu, Y.K.2
Agarwala, R.3
Schäffer, A.A.4
Altschul, S.F.5
-
45
-
-
33845679394
-
Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
-
DOI 10.1093/nar/gkl731
-
Yu YK, Gertz EM, Agarwala R, Schäffer AA, Altschul SF (2006) Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches. Nucleic Acids Res 34: 5966-5973. (Pubitemid 44941175)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.20
, pp. 5966-5973
-
-
Yu, Y.-K.1
Gertz, E.M.2
Agarwala, R.3
Schaffer, A.A.4
Altschul, S.F.5
-
46
-
-
34248578293
-
Assessment of phylogenomic and orthology approaches for phylogenetic inference
-
DOI 10.1093/bioinformatics/btm015
-
Dutilh BE, van Noort V, van der Heijden RTJM, Boekhout T, Snel B, et al. (2007) Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics 23: 815-824. (Pubitemid 47049915)
-
(2007)
Bioinformatics
, vol.23
, Issue.7
, pp. 815-824
-
-
Dutilh, B.E.1
Van Noort, V.2
Van Der Heijden R.T, J.M.3
Boekhout, T.4
Snel, B.5
Huynen, M.A.6
-
47
-
-
84859038699
-
Toward community standards in the quest for orthologs
-
Dessimoz C, Gabaldón T, Roos DS, Sonnhammer ELL, Herrero J, et al. (2012) Toward community standards in the quest for orthologs. Bioinformatics 28: 900-904.
-
(2012)
Bioinformatics
, vol.28
, pp. 900-904
-
-
Dessimoz, C.1
Gabaldón, T.2
Roos, D.S.3
Sonnhammer, E.L.L.4
Herrero, J.5
-
48
-
-
0001291140
-
A powerful non-homology method for the prediction of operons in prokaryotes
-
Moreno-Hagelsieb G, Collado-Vides J (2002) A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18 Suppl 1: S329-S336.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Moreno-Hagelsieb, G.1
Collado-Vides, J.2
-
49
-
-
84875634080
-
Phylogenomic clustering for selecting non-redundant genomes for comparative genomics
-
Moreno-Hagelsieb G, Wang Z, Walsh S, ElSherbiny A (2013) Phylogenomic clustering for selecting non-redundant genomes for comparative genomics. Bioinformatics 29: 947-949.
-
(2013)
Bioinformatics
, vol.29
, pp. 947-949
-
-
Moreno-Hagelsieb, G.1
Wang, Z.2
Walsh, S.3
ElSherbiny, A.4
|