-
1
-
-
0025878149
-
Amino acid substitution matrices from an information theoretic perspective
-
Altschul, S.F. 1991. Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219:555-665.
-
(1991)
J. Mol. Biol.
, vol.219
, pp. 555-665
-
-
Altschul, S.F.1
-
2
-
-
0028289467
-
Issues in searching molecular sequence databases
-
Altschul, S.F., M.S. Boguski, W.Gish and J.C. Wooten. 1994. Issues in searching molecular sequence databases. Nat. Genet. 6:119-129.
-
(1994)
Nat. Genet.
, vol.6
, pp. 119-129
-
-
Altschul, S.F.1
Boguski, M.S.2
Wooten, J.C.3
-
3
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., W. Gish, W. Miller, E. W. Myers and D.J. Lipman. 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.W.4
Lipman, D.J.5
-
4
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D.J. Lipman. 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
-
5
-
-
0031827544
-
Comparative accuracy of methods for protein sequence similarity search
-
Agarwal, P. and D.J. States. 1998. Comparative accuracy of methods for protein sequence similarity search. Bioinformatics 14:40-47.
-
(1998)
Bioinformatics
, vol.14
, pp. 40-47
-
-
Agarwal, P.1
States, D.J.2
-
6
-
-
0022474446
-
Maximum liklihood alignment of DNA sequences
-
Bishop, M. and E. Thompson. 1986. Maximum liklihood alignment of DNA sequences. J. Mol. Biol. 190:159-165.
-
(1986)
J. Mol. Biol.
, vol.190
, pp. 159-165
-
-
Bishop, M.1
Thompson, E.2
-
7
-
-
0026631005
-
The influence of nearest neighbor on the rate and pattern of spontaneous point mutations
-
Blake, R.D., S.T. Hess and J. Nicholson-Tuell. 1992. The influence of nearest neighbor on the rate and pattern of spontaneous point mutations. J. Mol. Evol. 34:189-200.
-
(1992)
J. Mol. Evol.
, vol.34
, pp. 189-200
-
-
Blake, R.D.1
Hess, S.T.2
Nicholson-Tuell, J.3
-
8
-
-
0030341663
-
-
D. States, P. Agarwal, T. Gaasterland, L. Hunter and R. Smith (Eds.), ISMB-4. AAAI Press, Menlo Park, CA
-
Bucher, P. and K. Hoffman. 1996. A sequence similarity algorithm based on a probabilistic interpretation of an alignment scoring system, p. 44-51. In D. States, P. Agarwal, T. Gaasterland, L. Hunter and R. Smith (Eds.), ISMB-4. AAAI Press, Menlo Park, CA.
-
(1996)
A Sequence Similarity Algorithm Based on a Probabilistic Interpretation of An Alignment Scoring System
, pp. 44-51
-
-
Bucher, P.1
Hoffman, K.2
-
9
-
-
0025277887
-
The significance of protein sequence similarities
-
R.F. Doolittle (Ed.), Academic Press, San Diego, CA
-
Collins, J.F. and A.F.W. Coulson. 1988. The significance of protein sequence similarities, p. 474-487. In R.F. Doolittle (Ed.), Methods in Enzymology. Vol. 183, Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences. Academic Press, San Diego, CA.
-
(1988)
Methods in Enzymology. Vol. 183, Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences
, vol.183
, pp. 474-487
-
-
Collins, J.F.1
Coulson, A.F.W.2
-
11
-
-
0000228203
-
A model of evolutionary change in proteins
-
M.O. Dayhoff (Ed.), National Biomedical Research Foundation, Washington DC
-
Dayhoff, M.O., R.M. Schwartz and B.C. Orcutt. 1978. A model of evolutionary change in proteins, p. 345-352. In M.O. Dayhoff (Ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington DC.
-
(1978)
Atlas of Protein Sequence and Structure
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
13
-
-
0028943946
-
The size distribution of insertions and deletions in human and rodent pseudogenes suggests logarithmic gap penalties for sequence alignment
-
Gu, X. and W.H. Li. 1995. The size distribution of insertions and deletions in human and rodent pseudogenes suggests logarithmic gap penalties for sequence alignment. J. Mol. Evol. 4:464-473.
-
(1995)
J. Mol. Evol.
, vol.4
, pp. 464-473
-
-
Gu, X.1
Li, W.H.2
-
14
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S. and J.G. Henikoff. 1992 Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA. 89:10915-10919.
-
(1992)
Proc. Natl. Acad. Sci. USA.
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
16
-
-
0028294455
-
Wide variations in neighbor-dependent substitution rates
-
Hess, S.T., J.D. Blake and R.D. Blake. 1994. Wide variations in neighbor-dependent substitution rates. J. Mol. Biol. 256:1022-1033.
-
(1994)
J. Mol. Biol.
, vol.256
, pp. 1022-1033
-
-
Hess, S.T.1
Blake, J.D.2
Blake, R.D.3
-
17
-
-
0027361123
-
A structural basis of sequence comparisons: An evaluation of scoring methodologies
-
Johnson, M.S. and J.P. Overington. 1993. A structural basis of sequence comparisons: an evaluation of scoring methodologies. J. Mol. Biol. 255:716-738.
-
(1993)
J. Mol. Biol.
, vol.255
, pp. 716-738
-
-
Johnson, M.S.1
Overington, J.P.2
-
18
-
-
0025259313
-
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
-
Karlin, S. and S.F. Altschul. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87:2264-2268.
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 2264-2268
-
-
Karlin, S.1
Altschul, S.F.2
-
19
-
-
0027175241
-
Applications and statistics for multiple high-scoring segments in molecular sequences
-
Karlin, S. and S.F. Altschul. 1993. Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl. Acad. Sci. USA 90:5873-5877.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 5873-5877
-
-
Karlin, S.1
Altschul, S.F.2
-
21
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequences of two proteins
-
Needleman, S.B. and C.D. Wunsch. 1970. A general method applicable to the search for similarities in the amino acid sequences 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
-
22
-
-
0026566796
-
Analysis of insertions/deletions in protein structures
-
Pascarella, S. and P. Argos. 1992. Analysis of insertions/deletions in protein structures. J. Mol. Biol. 20:461-471.
-
(1992)
J. Mol. Biol.
, vol.20
, pp. 461-471
-
-
Pascarella, S.1
Argos, P.2
-
23
-
-
0025950944
-
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
Pearson, W.R. 1991. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11:635-650.
-
(1991)
Genomics
, vol.11
, pp. 635-650
-
-
Pearson, W.R.1
-
24
-
-
0029006770
-
Comparison of methods for searching protein sequences databases
-
Pearson, W.R. 1995. Comparison of methods for searching protein sequences databases. Protein Science 4:1145-1160.
-
(1995)
Protein Science
, vol.4
, pp. 1145-1160
-
-
Pearson, W.R.1
-
25
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson, W.R. and D.J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA. 85:2444-2448.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
26
-
-
0000821965
-
On the theory and computation of evolutionary distances
-
Sellers, P.H. 1974. On the theory and computation of evolutionary distances. SIAM J. Appl. Math. 26:787-793.
-
(1974)
SIAM J. Appl. Math.
, vol.26
, pp. 787-793
-
-
Sellers, P.H.1
-
27
-
-
0018758632
-
Pattern recognition in genetic sequences
-
Sellers, P.H. 1979. Pattern recognition in genetic sequences. Proc. Natl. Acad. Sci. USA 76:3041-3041.
-
(1979)
Proc. Natl. Acad. Sci. USA
, vol.76
, pp. 3041-3041
-
-
Sellers, P.H.1
-
28
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith, T.F. and M.S. Waterman. 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
-
29
-
-
0022431785
-
The statistical distribution of nucleic acid similarities
-
Smith, T.F., M.C. Waterman and C. Burkes. 1985. The statistical distribution of nucleic acid similarities. Nucleic Acids Res. 13:645-656.
-
(1985)
Nucleic Acids Res.
, vol.13
, pp. 645-656
-
-
Smith, T.F.1
Waterman, M.C.2
Burkes, C.3
-
30
-
-
0002164370
-
Improved sensitivity of nucleic acid database search using application-specific scoring matrices methods
-
States, D.J., W. Gish and S.F. Altschul. 1991. Improved sensitivity of nucleic acid database search using application-specific scoring matrices methods. Methods Enzymol. 3:66-77.
-
(1991)
Methods Enzymol.
, vol.3
, pp. 66-77
-
-
States, D.J.1
Gish, W.2
Altschul, S.F.3
-
31
-
-
0026079507
-
An evolutionary model for maximum likelihood alignment of DNA sequences
-
Thorne, J.L., H. Kishino and J. Felsenstein. 1991. An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol Evol. 33:114-124.
-
(1991)
J. Mol Evol.
, vol.33
, pp. 114-124
-
-
Thorne, J.L.1
Kishino, H.2
Felsenstein, J.3
-
32
-
-
0028047892
-
Sequence alignment and penalty choice
-
Vingron, M. and M.S. Waterman. 1994. Sequence alignment and penalty choice. J. Mol. Biol. 235:1-12.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1-12
-
-
Vingron, M.1
Waterman, M.S.2
-
33
-
-
0023661088
-
A new algorithm for subsequence alignments with application to tRNA-rRNA comparisons
-
Waterman, M.S. and M. Eggert. 1987. A new algorithm for subsequence alignments with application to tRNA-rRNA comparisons. J. Mol. Biol. 197:723-728.
-
(1987)
J. Mol. Biol.
, vol.197
, pp. 723-728
-
-
Waterman, M.S.1
Eggert, M.2
|