-
1
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman, S. B. and Wunsch, C. D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453.
-
(1970)
J. Mol. Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
2
-
-
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
-
3
-
-
0024234855
-
CLUSTAL: A package for performing multiple sequence alignment on a microcomputer
-
Higgins, D. G. and Sharp, P. M. (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237-244.
-
(1988)
Gene
, vol.73
, pp. 237-244
-
-
Higgins, D.G.1
Sharp, P.M.2
-
4
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., Higgins, D. G., and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205-217.
-
(2000)
J. Mol. Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
5
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
6
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
Lee, C., Grasso, C., and Sharlow, M. F. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics 18, 452-464.
-
(2002)
Bioinformatics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
8
-
-
12344335569
-
DAGchainer: A tool for mining segmental genome duplications and synteny
-
Haas, B. J., Delcher, A. L., Wortman, J. R., and Salzberg, S. L. (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20, 3643-3646.
-
(2004)
Bioinformatics
, vol.20
, pp. 3643-3646
-
-
Haas, B.J.1
Delcher, A.L.2
Wortman, J.R.3
Salzberg, S.L.4
-
9
-
-
17444395994
-
Statistical detection of chromosomal homology using shared-gene density alone
-
Hampson, S. E., Gaut, B. S., and Baldi, P. (2005) Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics 21, 1339-1348.
-
(2005)
Bioinformatics
, vol.21
, pp. 1339-1348
-
-
Hampson, S.E.1
Gaut, B.S.2
Baldi, P.3
-
10
-
-
0037767267
-
LineUp: Statistical detection of chromosomal homology with application to plant comparative genomics
-
Hampson, S., McLysaght, A., Gaut, B., and Baldi, P. (2003) LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Res. 13, 999-1010.
-
(2003)
Genome Res
, vol.13
, pp. 999-1010
-
-
Hampson, S.1
McLysaght, A.2
Gaut, B.3
Baldi, P.4
-
11
-
-
0036211065
-
GRIMM: Genome rearrangements web server
-
Tesler, G. (2002) GRIMM: genome rearrangements web server. Bioinformatics 18, 492-493.
-
(2002)
Bioinformatics
, vol.18
, pp. 492-493
-
-
Tesler, G.1
-
12
-
-
0036940872
-
A novel approach to remote homology detection: Jumping alignments
-
Spang, R., Rehmsmeier, M., and Stoye, J. (2002) A novel approach to remote homology detection: Jumping alignments. Journal of Computational Biology 9, 747-760.
-
(2002)
Journal of Computational Biology
, vol.9
, pp. 747-760
-
-
Spang, R.1
Rehmsmeier, M.2
Stoye, J.3
-
13
-
-
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
-
14
-
-
0347724102
-
GRIL: Genome rearrangement and inversion locator
-
Darling, A. E., Mau, B., Blattner, F. R., and Perna, N. T. (2004) GRIL: genome rearrangement and inversion locator. Bioinformatics 20, 122-124.
-
(2004)
Bioinformatics
, vol.20
, pp. 122-124
-
-
Darling, A.E.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
15
-
-
36549049660
-
-
Durbin, R. (1998) Biological Sequence Analysis: Probabalistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK, pp. xi, 356.
-
Durbin, R. (1998) Biological Sequence Analysis: Probabalistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK, pp. xi, 356.
-
-
-
-
16
-
-
0034178257
-
Homology a personal view on some of the problems
-
Fitch, W. M. (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
-
17
-
-
20444394416
-
A Bayesian approach to the estimation of ancestral genome arrangements
-
Larget, B., Kadane, J. B., and Simon, D. L. (2005) A Bayesian approach to the estimation of ancestral genome arrangements. Mol. Phylogenet. Evol. 36, 214-223.
-
(2005)
Mol. Phylogenet. Evol
, vol.36
, pp. 214-223
-
-
Larget, B.1
Kadane, J.B.2
Simon, D.L.3
-
18
-
-
0036143403
-
Genome-scale evolution: Reconstructing gene orders in the ancestral species
-
Bourque, G. and Pevzner, P. A. (2002) Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12, 26-36.
-
(2002)
Genome Res
, vol.12
, pp. 26-36
-
-
Bourque, G.1
Pevzner, P.A.2
-
19
-
-
0042128756
-
Algorithms for multiple genome rearrangement by signed reversals
-
Wu, S. and Gu, X. (2003) Algorithms for multiple genome rearrangement by signed reversals. Pac. Symp. Biocomput. 363-374.
-
(2003)
Pac. Symp. Biocomput
, pp. 363-374
-
-
Wu, S.1
Gu, X.2
-
20
-
-
20744440507
-
ROBIN: A tool for genome rearrangement of block-interchanges
-
Lu, C. L., Wang, T. C., Lin, Y. C., and Tang, C. Y. (2005) ROBIN: a tool for genome rearrangement of block-interchanges. Bioinformatics 21, 2780-2782.
-
(2005)
Bioinformatics
, vol.21
, pp. 2780-2782
-
-
Lu, C.L.1
Wang, T.C.2
Lin, Y.C.3
Tang, C.Y.4
-
21
-
-
24044535485
-
Efficient sorting of genomic permutations by translocation, inversion and block interchange
-
Yancopoulos, S., Attie, O., and Friedberg, R. (2005) Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340-3346.
-
(2005)
Bioinformatics
, vol.21
, pp. 3340-3346
-
-
Yancopoulos, S.1
Attie, O.2
Friedberg, R.3
-
22
-
-
0037379673
-
Phylogeny estimation: Traditional and Bayesian approaches
-
Holder, M. and Lewis, P. O. (2003) Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4, 275-284.
-
(2003)
Nat. Rev. Genet
, vol.4
, pp. 275-284
-
-
Holder, M.1
Lewis, P.O.2
-
23
-
-
0242318328
-
Likelihood models of somatic mutation and codon substitution in cancer genes
-
Yang, Z., Ro, S., and Rannala, B. (2003) Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics 165, 695-705.
-
(2003)
Genetics
, vol.165
, pp. 695-705
-
-
Yang, Z.1
Ro, S.2
Rannala, B.3
-
24
-
-
33645798112
-
Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model
-
Lunter, G., Ponting, C. P., and Hein, J. (2006) Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model. PLoS Comput. Biol. 2, e5.
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Lunter, G.1
Ponting, C.P.2
Hein, J.3
-
25
-
-
3543051830
-
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
-
Darling, A. C., Mau, B., Blattner, F. R., and Perna, N. T. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403.
-
(2004)
Genome Res
, vol.14
, pp. 1394-1403
-
-
Darling, A.C.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
26
-
-
4944262040
-
Glocal alignment: Finding rearrangements during alignment
-
Brudno, M., Malde, S., Poliakov, A., et al. (2003) Glocal alignment: finding rearrangements during alignment. Bioinformatics 19, i54-i62.
-
(2003)
Bioinformatics
, vol.19
-
-
Brudno, M.1
Malde, S.2
Poliakov, A.3
-
27
-
-
12744253685
-
Mulan: Multiplesequence local alignment and visualization for studying function and evolution
-
Ovcharenko, I., Loots, G. G., Giardine, B. M., et al. (2005) Mulan: multiplesequence local alignment and visualization for studying function and evolution. Genome Res. 15, 184-194.
-
(2005)
Genome Res
, vol.15
, pp. 184-194
-
-
Ovcharenko, I.1
Loots, G.G.2
Giardine, B.M.3
-
28
-
-
33750441484
-
M-GCAT: Interactively and efficiency constructing large-scale multiple genome comparision frameworks in closely related species
-
Treangen, T. J. and Messeguer, X. (2006) M-GCAT: interactively and efficiency constructing large-scale multiple genome comparision frameworks in closely related species. BMC Bioinformatics 7, 433.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 433
-
-
Treangen, T.J.1
Messeguer, X.2
-
29
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz, S., Phillippy, A., Delcher, A. L., et al. (2004) Versatile and open software for comparing large genomes. Genome Biol. 5, R12.
-
(2004)
Genome Biol
, vol.5
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
-
30
-
-
0242470267
-
Efficient multiple genome alignment
-
Hohl, M., Kurtz, S., and Ohlebusch, E. (2002) Efficient multiple genome alignment. Bioinformatics 18, S312-S320.
-
(2002)
Bioinformatics
, vol.18
-
-
Hohl, M.1
Kurtz, S.2
Ohlebusch, E.3
-
31
-
-
1542748076
-
-
Aligning multiple genomic sequences with the threaded blockset aligner
-
Blanchette, M., Kent, W. J., Riemer, C., et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708-715.
-
(2004)
Genome Res
, vol.14
, pp. 708-715
-
-
Blanchette, M.1
Kent, W.J.2
Riemer, C.3
-
32
-
-
1842667852
-
MAVID: Constrained ancestral alignment of multiple sequences
-
Bray, N. and Pachter, L. (2004) MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693-699.
-
(2004)
Genome Res
, vol.14
, pp. 693-699
-
-
Bray, N.1
Pachter, L.2
-
33
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno, M., Do, C. B., Cooper, G. M., et al. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731.
-
(2003)
Genome Res
, vol.13
, pp. 721-731
-
-
Brudno, M.1
Do, C.B.2
Cooper, G.M.3
-
34
-
-
2442674056
-
Good spaced seeds for homology search
-
Choi, K. P., Zeng, F., and Zhang, L. (2004) Good spaced seeds for homology search. Bioinformatics 20, 1053-1059.
-
(2004)
Bioinformatics
, vol.20
, pp. 1053-1059
-
-
Choi, K.P.1
Zeng, F.2
Zhang, L.3
-
35
-
-
19544379902
-
Whole-genome prokaryotic phylogeny
-
Henz, S. R., Huson, D. H., Auch, A. F., Nieselt-Struwe, K., and Schuster, S. C. (2005) Whole-genome prokaryotic phylogeny. Bioinformatics 21, 2329-2335.
-
(2005)
Bioinformatics
, vol.21
, pp. 2329-2335
-
-
Henz, S.R.1
Huson, D.H.2
Auch, A.F.3
Nieselt-Struwe, K.4
Schuster, S.C.5
-
36
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
-
(1987)
Mol. Biol. Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
37
-
-
0030948139
-
Plague pneumonia disease caused by Yersinia pestis
-
Cleri, D. J., Vernaleo, J. R., Lombardi, L. J., et al. (1997) Plague pneumonia disease caused by Yersinia pestis. Semin. Respir. Infect. 12, 12-23.
-
(1997)
Semin. Respir. Infect
, vol.12
, pp. 12-23
-
-
Cleri, D.J.1
Vernaleo, J.R.2
Lombardi, L.J.3
-
38
-
-
0037793126
-
Evolution of pathogenic Yersinia, some lights in the dark
-
Carniel, E. (2003) Evolution of pathogenic Yersinia, some lights in the dark. Adv. Exp. Med. Biol. 529, 3-12.
-
(2003)
Adv. Exp. Med. Biol
, vol.529
, pp. 3-12
-
-
Carniel, E.1
-
39
-
-
4644293305
-
Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis
-
Chain, P. S., Carniel, E., Larimer, F. W., et al. (2004) Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 101, 13,826-13,831.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
-
-
Chain, P.S.1
Carniel, E.2
Larimer, F.W.3
-
40
-
-
22944434548
-
The evolution of flea-borne transmission in Yersinia pestis
-
Hinnebusch, B. J. (2005) The evolution of flea-borne transmission in Yersinia pestis. Curr. Issues Mol. Biol. 7, 197-212.
-
(2005)
Curr. Issues Mol. Biol
, vol.7
, pp. 197-212
-
-
Hinnebusch, B.J.1
-
41
-
-
0035945586
-
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
-
Perna, N. T., Plunkett, G., 3rd, Burland, V., et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529-533.
-
(2001)
Nature
, vol.409
, pp. 529-533
-
-
Perna, N.T.1
Plunkett 3rd, G.2
Burland, V.3
-
42
-
-
55449094978
-
Evidence of a large novel gene pool associated with prokaryotic genomic islands
-
Hsiao, W. W., Ung, K., Aeschliman, D., Bryan, J., Finlay, B. B., and Brinkman, F. S. (2005) Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet. 1, e62.
-
(2005)
PLoS Genet
, vol.1
-
-
Hsiao, W.W.1
Ung, K.2
Aeschliman, D.3
Bryan, J.4
Finlay, B.B.5
Brinkman, F.S.6
-
43
-
-
25444524604
-
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial pan-genome
-
Tettelin, H., Masignani, V., Cieslewicz, M. J., et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc. Natl. Acad. Sci. USA 102, 13,950-13,955.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
-
-
Tettelin, H.1
Masignani, V.2
Cieslewicz, M.J.3
-
44
-
-
0034034265
-
Evolution of the Gypsy endogenous retrovirus in the Drosophila melanogaster subgroup
-
Terzian, C., Ferraz, C., Demaille, J., and Bucheton, A. 2000) Evolution of the Gypsy endogenous retrovirus in the Drosophila melanogaster subgroup. Mol. Biol. Evol. 17, 908-914.
-
(2000)
Mol. Biol. Evol
, vol.17
, pp. 908-914
-
-
Terzian, C.1
Ferraz, C.2
Demaille, J.3
Bucheton, A.4
-
45
-
-
0036773353
-
CINEMA-MX: A modular multiple alignment editor
-
Lord, P. W., Selley, J. N., and Attwood, T. K. (2002) CINEMA-MX: a modular multiple alignment editor. Bioinformatics 18, 1402-1403.
-
(2002)
Bioinformatics
, vol.18
, pp. 1402-1403
-
-
Lord, P.W.1
Selley, J.N.2
Attwood, T.K.3
|