-
2
-
-
0345107239
-
Selection in the evolution of gene duplications
-
research0008.1
-
Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV: Selection in the evolution of gene duplications. Genome Biol. 2002, 3: research0008.1-0008.9. 10.1186/gb-2002-3-2-research0008. DOI: 10.1186/gb-2002-3-2-research0008
-
(2002)
Genome Biol
, vol.3
-
-
Kondrashov, F.A.1
Rogozin, I.B.2
Wolf, Y.I.3
Koonin, E.V.4
-
3
-
-
0037572262
-
On the nature of gene innovation: duplication patterns in microbial genomes
-
PID: 12716994, COI: 1:CAS:528:DC%2BD3sXkvFCgtbs%3D
-
Hooper SD, Berg OG: On the nature of gene innovation: duplication patterns in microbial genomes. Mol Biol Evol. 2003, 20: 945-954. 10.1093/molbev/msg101. DOI: 10.1093/molbev/msg101
-
(2003)
Mol Biol Evol
, vol.20
, pp. 945-954
-
-
Hooper, S.D.1
Berg, O.G.2
-
4
-
-
0034629478
-
Complete genome sequence of Neisseria meningitidisserogroup B strain MC58
-
PID: 10710307, COI: 1:CAS:528:DC%2BD3cXhvVWksbw%3D
-
Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, et al: Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. 2000, 287: 1809-1815. 10.1126/science.287.5459.1809. DOI: 10.1126/science.287.5459.1809
-
(2000)
Science
, vol.287
, pp. 1809-1815
-
-
Tettelin, H.1
Saunders, N.J.2
Heidelberg, J.3
Jeffries, A.C.4
Nelson, K.E.5
Eisen, J.A.6
Ketchum, K.A.7
Hood, D.W.8
Peden, J.F.9
Dodson, R.J.10
-
5
-
-
0032870941
-
Codon usage and lateral gene transfer in Bacillus subtilis
-
PID: 10508724, COI: 1:CAS:528:DyaK1MXntlCku7o%3D
-
Moszer I, Rocha EP, Danchin A: Codon usage and lateral gene transfer in Bacillus subtilis. Curr Opin Microbiol. 1999, 2: 524-528. 10.1016/S1369-5274(99)00011-9. DOI: 10.1016/S1369-5274(99)00011-9
-
(1999)
Curr Opin Microbiol
, vol.2
, pp. 524-528
-
-
Moszer, I.1
Rocha, E.P.2
Danchin, A.3
-
6
-
-
0026332291
-
Evidence for horizontal gene transfer in Escherichia colispeciation
-
PID: 1762151, COI: 1:CAS:528:DyaK38XnslOgsg%3D%3D
-
Medigue C, Rouxel T, Vigier P, Henaut A, Danchin A: Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol. 1991, 222: 851-856. DOI: 10.1016/0022-2836(91)90575-Q
-
(1991)
J Mol Biol
, vol.222
, pp. 851-856
-
-
Medigue, C.1
Rouxel, T.2
Vigier, P.3
Henaut, A.4
Danchin, A.5
-
7
-
-
0035106010
-
Phylogenetic analyses of two "archaeal" genes in Thermotoga maritimareveal multiple transfers between archaea and bacteria
-
PID: 11230537, COI: 1:CAS:528:DC%2BD3MXhvVKrtrs%3D
-
Nesbo CL, L'Haridon S, Stetter KO, Doolittle WF: Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol Biol Evol. 2001, 18: 362-375. DOI: 10.1093/oxfordjournals.molbev.a003812
-
(2001)
Mol Biol Evol
, vol.18
, pp. 362-375
-
-
Nesbo, C.L.1
L'Haridon, S.2
Stetter, K.O.3
Doolittle, W.F.4
-
8
-
-
0031736121
-
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles
-
PID: 9825671, COI: 1:CAS:528:DyaK1cXns1ynur8%3D
-
Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV: Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 1998, 14: 442-444. 10.1016/S0168-9525(98)01553-4. DOI: 10.1016/S0168-9525(98)01553-4
-
(1998)
Trends Genet
, vol.14
, pp. 442-444
-
-
Aravind, L.1
Tatusov, R.L.2
Wolf, Y.I.3
Walker, D.R.4
Koonin, E.V.5
-
9
-
-
0030994798
-
Amelioration of bacterial genomes: rates of change and exchange
-
PID: 9089078, COI: 1:CAS:528:DyaK2sXis12msLw%3D
-
Lawrence JG, Ochman H: Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol. 1997, 44: 383-397. DOI: 10.1007/PL00006158
-
(1997)
J Mol Evol
, vol.44
, pp. 383-397
-
-
Lawrence, J.G.1
Ochman, H.2
-
10
-
-
0032482924
-
Molecular archaeology of the Escherichia coligenome
-
PID: 9689094, COI: 1:CAS:528:DyaK1cXltlClsro%3D
-
Lawrence JG, Ochman H: Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA. 1998, 95: 9413-9417. 10.1073/pnas.95.16.9413. DOI: 10.1073/pnas.95.16.9413
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 9413-9417
-
-
Lawrence, J.G.1
Ochman, H.2
-
11
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
PID: 11076857, COI: 1:CAS:528:DC%2BD3cXosVWjtLw%3D
-
Garcia-Vallve S, Romeu A, Palau J: Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 2000, 10: 1719-1725. 10.1101/gr.130000. DOI: 10.1101/gr.130000
-
(2000)
Genome Res
, vol.10
, pp. 1719-1725
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
-
12
-
-
0036143446
-
Genomes in flux: the evolution of archaeal and proteobacterial gene content
-
PID: 11779827, COI: 1:CAS:528:DC%2BD38XksV2rsQ%3D%3D
-
Snel B, Bork P, Huynen MA: Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 2002, 12: 17-25. 10.1101/gr.176501. DOI: 10.1101/gr.176501
-
(2002)
Genome Res
, vol.12
, pp. 17-25
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
13
-
-
0033603539
-
Phylogenetic classification the universal tree
-
PID: 10381871, COI: 1:CAS:528:DyaK1MXkt1Kgsbs%3D
-
Doolittle WF: Phylogenetic classification the universal tree. Science. 1999, 284: 2124-2129. 10.1126/science.284.5423.2124. DOI: 10.1126/science.284.5423.2124
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
14
-
-
0036598066
-
Gene transfer in bacteria: speciation without species?
-
PID: 12167364
-
Lawrence JG: Gene transfer in bacteria: speciation without species?. Theor Popul Biol. 2002, 61: 449-460. 10.1006/tpbi.2002.1587. DOI: 10.1006/tpbi.2002.1587
-
(2002)
Theor Popul Biol
, vol.61
, pp. 449-460
-
-
Lawrence, J.G.1
-
15
-
-
0036898759
-
Prokaryotic evolution in light of gene transfer
-
PID: 12446813, COI: 1:CAS:528:DC%2BD38Xps12hsL4%3D
-
Gogarten JP, Doolittle WF, Lawrence JG: Prokaryotic evolution in light of gene transfer. Mol Biol Evol. 2002, 19: 2226-2238. DOI: 10.1093/oxfordjournals.molbev.a004046
-
(2002)
Mol Biol Evol
, vol.19
, pp. 2226-2238
-
-
Gogarten, J.P.1
Doolittle, W.F.2
Lawrence, J.G.3
-
16
-
-
0034252515
-
Something for everyone: horizontal gene transfer in evolution
-
PID: 11265763, COI: 1:CAS:528:DC%2BD3cXnt1yrsrY%3D
-
Kurland CG: Something for everyone: horizontal gene transfer in evolution. EMBO Rep. 2000, 1: 92-95. 10.1093/embo-reports/kvd042. DOI: 10.1093/embo-reports/kvd042
-
(2000)
EMBO Rep
, vol.1
, pp. 92-95
-
-
Kurland, C.G.1
-
17
-
-
0036899896
-
Evolution of microbial genomes: sequence acquisition and loss
-
PID: 12446817, COI: 1:CAS:528:DC%2BD38Xps12hsLo%3D
-
Berg OG, Kurland CG: Evolution of microbial genomes: sequence acquisition and loss. Mol Biol Evol. 2002, 19: 2265-2276. DOI: 10.1093/oxfordjournals.molbev.a004050
-
(2002)
Mol Biol Evol
, vol.19
, pp. 2265-2276
-
-
Berg, O.G.1
Kurland, C.G.2
-
18
-
-
0036892840
-
Gene import or deletion - a study of the difference genes in Escherichia colistrains K12 and O157:H7
-
PID: 12486532, COI: 1:CAS:528:DC%2BD38Xps1ehurs%3D
-
Hooper SD, Berg OG: Gene import or deletion - a study of the difference genes in Escherichia coli strains K12 and O157:H7. J Mol Evol. 2002, 55: 734-744. 10.1007/s00239-002-2369-2. DOI: 10.1007/s00239-002-2369-2
-
(2002)
J Mol Evol
, vol.55
, pp. 734-744
-
-
Hooper, S.D.1
Berg, O.G.2
-
19
-
-
0036176720
-
Detection of genes with atypical nucleotide sequence in microbial genomes
-
PID: 11847562, COI: 1:CAS:528:DC%2BD38XhsFKksrY%3D
-
Hooper SD, Berg OG: Detection of genes with atypical nucleotide sequence in microbial genomes. J Mol Evol. 2002, 54: 365-375. DOI: 10.1007/s00239-001-0051-8
-
(2002)
J Mol Evol
, vol.54
, pp. 365-375
-
-
Hooper, S.D.1
Berg, O.G.2
-
20
-
-
0023650543
-
The Codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications
-
PID: 3547335, COI: 1:CAS:528:DyaL2sXhtlejtrc%3D
-
Sharp PM, Li W-H: The Codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987, 15: 1281-1295. DOI: 10.1093/nar/15.3.1281
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.-H.2
-
21
-
-
0023762645
-
Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccaromyces pombe, Drosophila melanogaster and Homo sapiens: a review of the considerable within-species diversity
-
PID: 3138659, COI: 1:CAS:528:DyaL1cXlvVCqsbc%3D
-
Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, Wright F: Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccaromyces pombe, Drosophila melanogaster and Homo sapiens: a review of the considerable within-species diversity. Nucleic Acids Res. 1988, 16: 8207-8211. DOI: 10.1093/nar/16.17.8207
-
(1988)
Nucleic Acids Res
, vol.16
, pp. 8207-8211
-
-
Sharp, P.M.1
Cowe, E.2
Higgins, D.G.3
Shields, D.C.4
Wolfe, K.H.5
Wright, F.6
-
22
-
-
0034882455
-
Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes
-
PID: 11504864, COI: 1:CAS:528:DC%2BD3MXmt12hsLk%3D
-
Guindon S, Perriere G: Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes. Mol Biol Evol. 2001, 18: 1838-1840. DOI: 10.1093/oxfordjournals.molbev.a003972
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1838-1840
-
-
Guindon, S.1
Perriere, G.2
-
23
-
-
15444350252
-
The complete genome sequence of Escherichia coliK-12
-
PID: 9278503, COI: 1:CAS:528:DyaK2sXlvVGnu78%3D
-
Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, et al: The complete genome sequence of Escherichia coli K-12. Science. 1997, 277: 1453-1474. 10.1126/science.277.5331.1453. DOI: 10.1126/science.277.5331.1453
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
Riley, M.6
Collado-Vides, J.7
Glasner, J.D.8
Rode, C.K.9
Mayhew, G.F.10
-
24
-
-
0035945586
-
Genome sequence of enterohaemorrhagic Escherichia coliO157:H7
-
PID: 11206551, COI: 1:CAS:528:DC%2BD3MXpvVeksA%3D%3D
-
Perna NT, Plunkett G, Burland V, Mau BM, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, et al: Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 2001, 409: 529-533. 10.1038/35054089. DOI: 10.1038/35054089
-
(2001)
Nature
, vol.409
, pp. 529-533
-
-
Perna, N.T.1
Plunkett, G.2
Burland, V.3
Mau, B.M.4
Glasner, J.D.5
Rose, D.J.6
Mayhew, G.F.7
Evans, P.S.8
Gregor, J.9
Kirkpatrick, H.A.10
-
25
-
-
18644378721
-
Genome sequence of Shigella flexneri 2a, insights into pathogenicity through comparison with genomes of Escherichia coliK12 and O157
-
PID: 12384590, COI: 1:CAS:528:DC%2BD38Xot1Cju7w%3D
-
Jin Q, Yuan ZH, Xu JG, Wang Y, Shen Y, Lu WC, Wang JH, Liu H, Yang J, Yang F, et al: Genome sequence of Shigella flexneri 2a, insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 2002, 30: 4432-4441. 10.1093/nar/gkf566. DOI: 10.1093/nar/gkf566
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4432-4441
-
-
Jin, Q.1
Yuan, Z.H.2
Xu, J.G.3
Wang, Y.4
Shen, Y.5
Lu, W.C.6
Wang, J.H.7
Liu, H.8
Yang, J.9
Yang, F.10
-
26
-
-
0035950182
-
Complete genome sequence of Salmonella enterica serovar TyphimuriumLT2
-
PID: 11677609, COI: 1:CAS:528:DC%2BD3MXotFyrtL4%3D
-
McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, et al: Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature. 2001, 413: 852-856. 10.1038/35101614. DOI: 10.1038/35101614
-
(2001)
Nature
, vol.413
, pp. 852-856
-
-
McClelland, M.1
Sanderson, K.E.2
Spieth, J.3
Clifton, S.W.4
Latreille, P.5
Courtney, L.6
Porwollik, S.7
Ali, J.8
Dante, M.9
Du, F.10
-
27
-
-
0035950154
-
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar TyphiCT18
-
PID: 11677608, COI: 1:CAS:528:DC%2BD3MXotFyrt7k%3D
-
Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MTG, et al: Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature. 2001, 413: 848-852. 10.1038/35101607. DOI: 10.1038/35101607
-
(2001)
Nature
, vol.413
, pp. 848-852
-
-
Parkhill, J.1
Dougan, G.2
James, K.D.3
Thomson, N.R.4
Pickard, D.5
Wain, J.6
Churcher, C.7
Mungall, K.L.8
Bentley, S.D.9
Holden, M.T.G.10
-
28
-
-
0030731108
-
The complete genome sequence of the gram-positive bacterium Bacillus subtilis
-
PID: 9384377, COI: 1:CAS:528:DyaK2sXnsVyqtrY%3D
-
Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, et al: The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997, 390: 249-256. 10.1038/36786. DOI: 10.1038/36786
-
(1997)
Nature
, vol.390
, 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
-
29
-
-
0034327380
-
Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis
-
PID: 11058132, COI: 1:CAS:528:DC%2BD3cXovFOiu7Y%3D
-
Takami H, Nakasone K, Takaki Y, Maeno G, Sasaki Y, Masui N, Fuji F, Hirama C, Nakamura Y, Ogasawara N, et al: Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res. 2000, 28: 4317-4331. 10.1093/nar/28.21.4317. DOI: 10.1093/nar/28.21.4317
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 4317-4331
-
-
Takami, H.1
Nakasone, K.2
Takaki, Y.3
Maeno, G.4
Sasaki, Y.5
Masui, N.6
Fuji, F.7
Hirama, C.8
Nakamura, Y.9
Ogasawara, N.10
-
30
-
-
0037154260
-
Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater
-
PID: 11792842, COI: 1:CAS:528:DC%2BD38Xht1Witr0%3D
-
Shimizu T, Ohtani K, Hirakawa H, Ohshima K, Yamashita A, Shiba T, Ogasawara N, Hattori M, Kuhara S, Hayashi H: Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci USA. 2002, 99: 996-1001. 10.1073/pnas.022493799. DOI: 10.1073/pnas.022493799
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 996-1001
-
-
Shimizu, T.1
Ohtani, K.2
Hirakawa, H.3
Ohshima, K.4
Yamashita, A.5
Shiba, T.6
Ogasawara, N.7
Hattori, M.8
Kuhara, S.9
Hayashi, H.10
-
31
-
-
0034902930
-
Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum
-
PID: 11466286, COI: 1:CAS:528:DC%2BD3MXlslKkt7g%3D
-
Nolling J, Breton G, Omelchenko MV, Markarova KS, Zeng Q, Gibson R, Lee HM, Dubois J, Qiu D, Hitti J, et al: Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol. 2001, 183: 4823-4838. 10.1128/JB.183.16.4823-4838.2001. DOI: 10.1128/JB.183.16.4823-4838.2001
-
(2001)
J Bacteriol
, vol.183
, pp. 4823-4838
-
-
Nolling, J.1
Breton, G.2
Omelchenko, M.V.3
Markarova, K.S.4
Zeng, Q.5
Gibson, R.6
Lee, H.M.7
Dubois, J.8
Qiu, D.9
Hitti, J.10
-
32
-
-
0035925904
-
Whole genome sequencing of methicillin-resistant Staphylococcus aureus
-
PID: 11418146, COI: 1:CAS:528:DC%2BD3MXjvVClur0%3D
-
Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, Cui L, Oguchi A, Aoki K, Nagai Y, et al: Whole genome sequencing of methicillin-resistant Staphylococcus aureus. Lancet. 2001, 357: 1225-1240. 10.1016/S0140-6736(00)04403-2. DOI: 10.1016/S0140-6736(00)04403-2
-
(2001)
Lancet
, vol.357
, pp. 1225-1240
-
-
Kuroda, M.1
Ohta, T.2
Uchiyama, I.3
Baba, T.4
Yuzawa, H.5
Kobayashi, I.6
Cui, L.7
Oguchi, A.8
Aoki, K.9
Nagai, Y.10
-
33
-
-
0037172403
-
Genome virulence determinants of high virulence community-acquired MRSA
-
PID: 12044378, COI: 1:CAS:528:DC%2BD38XktVaku7w%3D
-
Baba T, Takeuchi F, Kuroda M, Yuzawa H, Aoki K, Oguchi A, Nagai Y, Iwama N, Asano K, Naimi T, et al: Genome virulence determinants of high virulence community-acquired MRSA. Lancet. 2002, 359: 1819-1827. 10.1016/S0140-6736(02)08713-5. DOI: 10.1016/S0140-6736(02)08713-5
-
(2002)
Lancet
, vol.359
, pp. 1819-1827
-
-
Baba, T.1
Takeuchi, F.2
Kuroda, M.3
Yuzawa, H.4
Aoki, K.5
Oguchi, A.6
Nagai, Y.7
Iwama, N.8
Asano, K.9
Naimi, T.10
-
34
-
-
0034739007
-
Complete genome sequence of Pseudomonas aeruginosaPA01, an opportunistic pathogen
-
PID: 10984043, COI: 1:CAS:528:DC%2BD3cXmtlKqsrY%3D
-
Stover CK, Pham X-QT, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FSL, Hufnagle WO, Kowalik DJ, Lagrou M, et al: Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature. 2000, 406: 959-964. 10.1038/35023079. DOI: 10.1038/35023079
-
(2000)
Nature
, vol.406
, pp. 959-964
-
-
Stover, C.K.1
Pham, X.-Q.T.2
Erwin, A.L.3
Mizoguchi, S.D.4
Warrener, P.5
Hickey, M.J.6
Brinkman, F.S.L.7
Hufnagle, W.O.8
Kowalik, D.J.9
Lagrou, M.10
-
35
-
-
85182683650
-
-
Genome Sequencing Center. [http://genome.wustl.edu]
-
-
-
-
36
-
-
0025183708
-
Basic local alignment search tool
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PID: 2231712, COI: 1:CAS:528:DyaK3MXitVGmsA%3D%3D
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Altschul SF, Gish W, Miller M, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. 10.1006/jmbi.1990.9999. DOI: 10.1016/S0022-2836(05)80360-2
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(1990)
J Mol Biol
, vol.215
, pp. 403-410
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Altschul, S.F.1
Gish, W.2
Miller, M.3
Myers, E.W.4
Lipman, D.J.5
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