-
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
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
3
-
-
0034623005
-
T-Coffee: A novel algorithm for multiple sequence alignment
-
Notredame, C., Higgins, D., and Heringa, J. (2000) T-Coffee: a novel algorithm for multiple sequence alignment. J. Mol. Biol. 302, 205-217.
-
(2000)
J. Mol. Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.2
Heringa, J.3
-
5
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. M., and Lipman, D. J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.M.4
Lipman, D.J.5
-
6
-
-
0030801002
-
Gapped BLAST and PSIBLAST: A new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schärfer, A. A., et al. (1997) Gapped BLAST and PSIBLAST: 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
Schärfer, A.A.3
-
7
-
-
0027912333
-
Detecting subtle sequence signals: A gibbs sampling strategy for multiple alignment
-
Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F., and Wootton, J. C. (1993) Detecting subtle sequence signals: a gibbs sampling strategy for multiple alignment. Science 262, 208-214.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.F.5
Wootton, J.C.6
-
8
-
-
0037398368
-
LAGAN and multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno, M., Do, C., Cooper, G., 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.2
Cooper, G.3
-
9
-
-
0242470267
-
Efficient multiple genome alignment
-
Höhl, M., Kurtz, S., and Ohlebusch, E. (2002) Efficient multiple genome alignment. Bioinformatics 18, 312S-320S.
-
(2002)
Bioinformatics
, vol.18
-
-
Höhl, M.1
Kurtz, S.2
Ohlebusch, E.3
-
10
-
-
0033153375
-
Alignment of whole genomes
-
Delcher, A. L., Kasif, S., Fleischmann, R. D., Peterson, J., White, O., and Salzberg, S. L. (1999) Alignment of whole genomes. Nucleic Acids Res. 27, 2369-2376.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2369-2376
-
-
Delcher, A.L.1
Kasif, S.2
Fleischmann, R.D.3
Peterson, J.4
White, O.5
Salzberg, S.L.6
-
11
-
-
0042121222
-
MAVID multiple alignment server
-
Bray, N., and Pachter, L. (2003) MAVID multiple alignment server. Nucleic Acids Res. 31, 3525-3526.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3525-3526
-
-
Bray, N.1
Pachter, L.2
-
12
-
-
0029861894
-
Multiple DNA and protein sequence alignment based on segment-to-segment comparison
-
Morgenstern, B., Dress, A. W. M., and Werner, T. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. USA 93, 12,098-12,103.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
-
-
Morgenstern, B.1
Dress, A.W.M.2
Werner, T.3
-
13
-
-
3242891684
-
DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ
-
Morgenstern, B. (2004) DIALIGN: Multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res. 32, W33-W36.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Morgenstern, B.1
-
14
-
-
0031854952
-
DIALIGN: Finding local similarities by multiple sequence alignment
-
Morgenstern, B., Frech, K., Dress, A. W. M., and Werner, T. (1998) DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 14, 290-294.
-
(1998)
Bioinformatics
, vol.14
, pp. 290-294
-
-
Morgenstern, B.1
Frech, K.2
Dress, A.W.M.3
Werner, T.4
-
15
-
-
0032945593
-
DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
-
Morgenstern, B. (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211-218.
-
(1999)
Bioinformatics
, vol.15
, pp. 211-218
-
-
Morgenstern, B.1
-
16
-
-
1842679836
-
Surveying phylogenetic footprints in large gene clusters: Applications to Hox cluster duplications
-
Prohaska, S. J., Fried, C., Flamm, C., Wagner, G., and Stadler, P. F. (2004) Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications. Mol. Phyl. Evol. 31, 581-604.
-
(2004)
Mol. Phyl. Evol
, vol.31
, pp. 581-604
-
-
Prohaska, S.J.1
Fried, C.2
Flamm, C.3
Wagner, G.4
Stadler, P.F.5
-
17
-
-
6344274712
-
Divergence of conserved non-coding sequences: Rate estimates and relative rate tests
-
Wagner, G. P., Fried, C., Prohaska, S. J., and Stadler, P. F. (2004) Divergence of conserved non-coding sequences: rate estimates and relative rate tests. Mol. Biol. Evol. 21, 2116-2121.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 2116-2121
-
-
Wagner, G.P.1
Fried, C.2
Prohaska, S.J.3
Stadler, P.F.4
-
18
-
-
0036107903
-
Discovery of regulatory elements by a computationalmethod for phylogenetic footprinting
-
Blanchette, M. and Tompa, M. (2002) Discovery of regulatory elements by a computationalmethod for phylogenetic footprinting. Genome Res. 12, 739-748.
-
(2002)
Genome Res
, vol.12
, pp. 739-748
-
-
Blanchette, M.1
Tompa, M.2
-
19
-
-
0033972132
-
Analysis of vertebrate SCL loci identifies conserved enhancers
-
Göttgens, B., Barton, L. M., Gilbert, J. G. R., et al. (2000) Analysis of vertebrate SCL loci identifies conserved enhancers. Nat. Biotechnol. 18, 181-186.
-
(2000)
Nat. Biotechnol
, vol.18
, pp. 181-186
-
-
Göttgens, B.1
Barton, L.M.2
Gilbert, J.G.R.3
-
20
-
-
0035154384
-
Long-range comparison of human and mouse SCL loci: Localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences
-
Göttgens, B., Gilbert, J. G. R., Barton, L. M., et al. (2001) Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res. 11, 87-97.
-
(2001)
Genome Res
, vol.11
, pp. 87-97
-
-
Göttgens, B.1
Gilbert, J.G.R.2
Barton, L.M.3
-
21
-
-
0036110293
-
Transcriptional regulation of the stem cell leukemia gene (SCL) comparative analysis of five vertebrate SCL loci
-
Göttgens, B., Barton, L., Chapman, M., et al. (2002) Transcriptional regulation of the stem cell leukemia gene (SCL) comparative analysis of five vertebrate SCL loci. Genome Res. 12, 749-759.
-
(2002)
Genome Res
, vol.12
, pp. 749-759
-
-
Göttgens, B.1
Barton, L.2
Chapman, M.3
-
22
-
-
0037343446
-
Comparative and functional analysis of LYLl loci establish marsupial sequences as a model for phylogenetic footprinting
-
Chapman, M. A., Charchar, F. J., Kinston, S., et al. (2003) Comparative and functional analysis of LYLl loci establish marsupial sequences as a model for phylogenetic footprinting. Genomics 81, 249-259.
-
(2003)
Genomics
, vol.81
, pp. 249-259
-
-
Chapman, M.A.1
Charchar, F.J.2
Kinston, S.3
-
23
-
-
0345301960
-
Rapid development of nucleic acid diagnostics
-
Fitch, J. P., Gardner, S. N., Kuczmarski, T. A., et al. (2002) Rapid development of nucleic acid diagnostics. Proc. IEEE 90, 1708-1721.
-
(2002)
Proc. IEEE
, vol.90
, pp. 1708-1721
-
-
Fitch, J.P.1
Gardner, S.N.2
Kuczmarski, T.A.3
-
24
-
-
0142056169
-
An applicationsfocused review of comparative genomics tools: Capabilities, limitations, and future challenges
-
Chain, P., Kurtz, S., Ohlebusch, E., and Slezak, T. (2003) An applicationsfocused review of comparative genomics tools: capabilities, limitations, and future challenges. Brief. Bioinform. 4, 105-123.
-
(2003)
Brief. Bioinform
, vol.4
, pp. 105-123
-
-
Chain, P.1
Kurtz, S.2
Ohlebusch, E.3
Slezak, T.4
-
25
-
-
0036455972
-
AGenDA: Gene prediction by comparative sequence analysis
-
Rinner, O. and Morgenstern, B. (2002) AGenDA: gene prediction by comparative sequence analysis. In Silico Biol. 2, 195-205.
-
(2002)
In Silico Biol
, vol.2
, pp. 195-205
-
-
Rinner, O.1
Morgenstern, B.2
-
26
-
-
33645161645
-
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
-
Stanke, M., Schöffmann, O., Morgenstern, B., and Waack, S. (2006) Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 62
-
-
Stanke, M.1
Schöffmann, O.2
Morgenstern, B.3
Waack, S.4
-
27
-
-
33748674197
-
AUGUSTUS+ at EGASP: Using EST, protein and genomic alignments for improved gene prediction in the human genome
-
Stanke, M., Tzvetkova, A., and Morgenstern, B. (2006) AUGUSTUS+ at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol. 7, 1-8.
-
(2006)
Genome Biol
, vol.7
, pp. 1-8
-
-
Stanke, M.1
Tzvetkova, A.2
Morgenstern, B.3
-
28
-
-
2942516151
-
Benchmarking tools for the alignment of functional noncoding DNA
-
Pollard, D. A., Bergman, C. M., Stoye, J., Celniker, S. E., and Eisen, M. B. (2004) Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5, 6.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 6
-
-
Pollard, D.A.1
Bergman, C.M.2
Stoye, J.3
Celniker, S.E.4
Eisen, M.B.5
-
29
-
-
0036300594
-
Exon discovery by genomic sequence alignment
-
Morgenstern, B., Rinner, O., Abdeddai'm, S., Haase, D., Mayer, K., Dress, A., and Mewes, H. -W. (2002) Exon discovery by genomic sequence alignment. Bioinformatics 18, 777-787.
-
(2002)
Bioinformatics
, vol.18
, pp. 777-787
-
-
Morgenstern, B.1
Rinner, O.2
Abdeddai'm, S.3
Haase, D.4
Mayer, K.5
Dress, A.6
Mewes, H.-W.7
-
30
-
-
16344379173
-
Multiple sequence alignment with user-defined constraints at GOBICS
-
Morgenstern, B., Werner, N., Prohaska, S. J., et al. (2005) Multiple sequence alignment with user-defined constraints at GOBICS. Bioinformatics 21, 1271-1273.
-
(2005)
Bioinformatics
, vol.21
, pp. 1271-1273
-
-
Morgenstern, B.1
Werner, N.2
Prohaska, S.J.3
-
31
-
-
34248363117
-
Multiple sequence alignment with user-defined anchor points
-
Morgenstern, B., Prohaska, S. J., Pöhler, D., and Stadler, P. F. (2006) Multiple sequence alignment with user-defined anchor points. Algorithms Mol. Biol. 1, 6.
-
(2006)
Algorithms Mol. Biol
, vol.1
, pp. 6
-
-
Morgenstern, B.1
Prohaska, S.J.2
Pöhler, D.3
Stadler, P.F.4
-
32
-
-
2942603015
-
Fast and sensitive multiple alignment of large genomic sequences
-
Brudno, M., Chapman, M., Göttgens, B., Batzoglou, S., and Morgenstern, B. (2003) Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics 4, 66.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 66
-
-
Brudno, M.1
Chapman, M.2
Göttgens, B.3
Batzoglou, S.4
Morgenstern, B.5
-
33
-
-
3242889413
-
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences
-
Brudno, M., Steinkamp, R., and Morgenstern, B. (2004) The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Res. 32, W41-W44.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Brudno, M.1
Steinkamp, R.2
Morgenstern, B.3
-
34
-
-
23144450376
-
Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC
-
Pöhler, D., Werner, N., Steinkamp, R., and Morgenstern, B. (2005) Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC. Nuc. Acids Res. 33, W523-W524.
-
(2005)
Nuc. Acids Res
, vol.33
-
-
Pöhler, D.1
Werner, N.2
Steinkamp, R.3
Morgenstern, B.4
-
35
-
-
13244271404
-
ABC: Software for interactive browsing of genomic multiple sequence alignment data
-
Cooper, G. M., Singaravelu, S. A. G., and Sidow, A. (2004) ABC: software for interactive browsing of genomic multiple sequence alignment data. BMC Bioinformatics 5, 192.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 192
-
-
Cooper, G.M.1
Singaravelu, S.A.G.2
Sidow, A.3
|