-
1
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman S., and Wunsch C. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 42 (1970) 443-453
-
(1970)
J. Mol. Biol.
, vol.42
, pp. 443-453
-
-
Needleman, S.1
Wunsch, C.2
-
2
-
-
34547577318
-
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
-
Chung Y.S., Lee W.H., Tang C.Y., and Lu C.L. RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints. Nucleic Acids Res. 35 (2007) W639-W644
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Chung, Y.S.1
Lee, W.H.2
Tang, C.Y.3
Lu, C.L.4
-
3
-
-
33747829924
-
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
-
Armougom F., Moretti S., Poirot O., Audic S., Dumas P., Schaeli B., Keduas V., and Notredame C. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. 34 (2006) W604-W608
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Armougom, F.1
Moretti, S.2
Poirot, O.3
Audic, S.4
Dumas, P.5
Schaeli, B.6
Keduas, V.7
Notredame, C.8
-
4
-
-
12344295510
-
A probabilistic measure for alignment-free sequence comparison
-
Pham T.D., and Zuegg J. A probabilistic measure for alignment-free sequence comparison. Bioinformatics 20 (2004) 3455-3461
-
(2004)
Bioinformatics
, vol.20
, pp. 3455-3461
-
-
Pham, T.D.1
Zuegg, J.2
-
5
-
-
0025340372
-
Chaos game representation of gene structure
-
Jeffrey H.J. Chaos game representation of gene structure. Nucleic Acids Res. 18 (1990) 2163-2170
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 2163-2170
-
-
Jeffrey, H.J.1
-
6
-
-
0035016060
-
Analysis of genomic sequences by chaos game representation
-
Almeida J.S., Carrico J.A., Maretzek A., Noble P.A., and Fletcher M. Analysis of genomic sequences by chaos game representation. Bioinformatics 17 (2001) 429-437
-
(2001)
Bioinformatics
, vol.17
, pp. 429-437
-
-
Almeida, J.S.1
Carrico, J.A.2
Maretzek, A.3
Noble, P.A.4
Fletcher, M.5
-
7
-
-
0032823783
-
Genomic signature: characterization and classification of species assessed by chaos game representation of sequences
-
Deschavanne P.J., Giron A., Vilain J., Fagot G., and Fertil B. Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol. Biol. Evol. 16 (1999) 1391-1399
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1391-1399
-
-
Deschavanne, P.J.1
Giron, A.2
Vilain, J.3
Fagot, G.4
Fertil, B.5
-
8
-
-
0037315735
-
Evolutionary implications of microbial genome tetranucleotide frequency biases
-
Pride D.T., Meinersmann R.J., Wassenaar T.M., and Blaser M.J. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res. 13 (2003) 145-158
-
(2003)
Genome Res.
, vol.13
, pp. 145-158
-
-
Pride, D.T.1
Meinersmann, R.J.2
Wassenaar, T.M.3
Blaser, M.J.4
-
9
-
-
14744286093
-
The spectrum of genomic signatures: from dinucleotides to chaos game representation
-
Wang Y., Hill K., Singh S., and Kari L. The spectrum of genomic signatures: from dinucleotides to chaos game representation. Gene 346 (2005) 173-185
-
(2005)
Gene
, vol.346
, pp. 173-185
-
-
Wang, Y.1
Hill, K.2
Singh, S.3
Kari, L.4
-
10
-
-
28844458060
-
Exploration of phylogenetic data using a global sequence analysis method
-
Chapus C., Dufraigne C., Edwards S., Giron A., Fertil B., and Deschavanne P. Exploration of phylogenetic data using a global sequence analysis method. BMC Evol. Biol. 5 (2005) 63
-
(2005)
BMC Evol. Biol.
, vol.5
, pp. 63
-
-
Chapus, C.1
Dufraigne, C.2
Edwards, S.3
Giron, A.4
Fertil, B.5
Deschavanne, P.6
-
11
-
-
33745667975
-
Chaos game representation for comparison of whole genomes
-
Joseph J., and Sasikumar R. Chaos game representation for comparison of whole genomes. BMC Bioinformatics 7 (2006) 243
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 243
-
-
Joseph, J.1
Sasikumar, R.2
-
12
-
-
19744383764
-
Detection and characterization of horizontal transfers in prokaryotes using genomic signature
-
Dufraigne C., Fertil B., Lespinats S., Giron A., and Deschavanne P. Detection and characterization of horizontal transfers in prokaryotes using genomic signature. Nucleic Acids Res. 33 (2005) e6
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Dufraigne, C.1
Fertil, B.2
Lespinats, S.3
Giron, A.4
Deschavanne, P.5
-
13
-
-
4344670204
-
Application of tetranucleotide frequencies for the assignment of genomic fragments
-
Teeling H., Meyerdierks A., Bauer M., Amann R., and Glöckner F.O. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ. Microbiol. 6 (2004) 938-947
-
(2004)
Environ. Microbiol.
, vol.6
, pp. 938-947
-
-
Teeling, H.1
Meyerdierks, A.2
Bauer, M.3
Amann, R.4
Glöckner, F.O.5
-
14
-
-
0038648028
-
Quantifying the species-specificity in genomic signatures, synonymous, codon choice, amino acid usage and G + C content
-
Sandberg R., Bränden C.-I., Ernberg I., and Cöster J. Quantifying the species-specificity in genomic signatures, synonymous, codon choice, amino acid usage and G + C content. Gene 311 (2003) 35-42
-
(2003)
Gene
, vol.311
, pp. 35-42
-
-
Sandberg, R.1
Bränden, C.-I.2
Ernberg, I.3
Cöster, J.4
-
15
-
-
0028675409
-
Chaos game representation of protein structures
-
Fiser A., Tusnady G.E., and Simon I. Chaos game representation of protein structures. J. Mol. Graph. 12 (1994) 302-304
-
(1994)
J. Mol. Graph.
, vol.12
, pp. 302-304
-
-
Fiser, A.1
Tusnady, G.E.2
Simon, I.3
-
16
-
-
0344835813
-
Representation of amino acid sequences as two-dimensional point patterns
-
Pleissner K.P., Wernisch L., Oswald H., and Fleck E. Representation of amino acid sequences as two-dimensional point patterns. Electrophoresis 18 (1997) 2709-2713
-
(1997)
Electrophoresis
, vol.18
, pp. 2709-2713
-
-
Pleissner, K.P.1
Wernisch, L.2
Oswald, H.3
Fleck, E.4
-
18
-
-
0345256581
-
Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses
-
Yu Z.G., Anh V., and Lau K.S. Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses. J. Theor. Biol. 226 (2004) 341-348
-
(2004)
J. Theor. Biol.
, vol.226
, pp. 341-348
-
-
Yu, Z.G.1
Anh, V.2
Lau, K.S.3
-
19
-
-
0002946570
-
Universal sequence map (USM) of arbitrary discrete sequences
-
Almeida J.S., and Vinga S. Universal sequence map (USM) of arbitrary discrete sequences. BMC Bioinformatics 3 (2002) 6
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 6
-
-
Almeida, J.S.1
Vinga, S.2
-
20
-
-
0642311812
-
Efficient Boolean implementation of universal sequence maps (bUSM)
-
Schwacke J., and Almeida J.S. Efficient Boolean implementation of universal sequence maps (bUSM). BMC Bioinformatics 3 (2002) 28
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 28
-
-
Schwacke, J.1
Almeida, J.S.2
-
21
-
-
34248384741
-
Computing distribution of scale independent motifs in biological sequences
-
Almeida J.S., and Vinga S. Computing distribution of scale independent motifs in biological sequences. Algorithms Mol Biol. 1 (2006) 18
-
(2006)
Algorithms Mol Biol.
, vol.1
, pp. 18
-
-
Almeida, J.S.1
Vinga, S.2
-
22
-
-
2542458612
-
Classification of nuclear receptors based on amino acid composition and dipeptide composition
-
Bhasin M., and Raghava G.P. Classification of nuclear receptors based on amino acid composition and dipeptide composition. J. Biol. Chem. 279 (2004) 23262-23266
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 23262-23266
-
-
Bhasin, M.1
Raghava, G.P.2
-
23
-
-
17644389617
-
Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search
-
Garg A., Bhasin M., and Raghava G.P. Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search. J. Biol. Chem. 280 (2005) 14427-14432
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 14427-14432
-
-
Garg, A.1
Bhasin, M.2
Raghava, G.P.3
-
24
-
-
25444464110
-
Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein
-
Raghava G.P., and Han J.H. Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein. BMC Bioinformatics 6 (2005) 59
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 59
-
-
Raghava, G.P.1
Han, J.H.2
-
25
-
-
0033554601
-
A key driving force in determination of protein structural classes
-
Chou K.C. A key driving force in determination of protein structural classes. Biochem. Biophys. Res. Commun. 264 (1999) 216-224
-
(1999)
Biochem. Biophys. Res. Commun.
, vol.264
, pp. 216-224
-
-
Chou, K.C.1
-
26
-
-
33644842082
-
Prediction of protein secondary structure content using amino acid composition and evolutionary information
-
Lee S., Lee B.C., and Kim D. Prediction of protein secondary structure content using amino acid composition and evolutionary information. Proteins 62 (2006) 1107-1114
-
(2006)
Proteins
, vol.62
, pp. 1107-1114
-
-
Lee, S.1
Lee, B.C.2
Kim, D.3
-
28
-
-
4444273377
-
Protein homology detection using string alignment kernels
-
Saigo H., Vert J.P., Ueda N., and Akutsu T. Protein homology detection using string alignment kernels. Bioinformatics 20 (2004) 1682-1689
-
(2004)
Bioinformatics
, vol.20
, pp. 1682-1689
-
-
Saigo, H.1
Vert, J.P.2
Ueda, N.3
Akutsu, T.4
-
29
-
-
33644876020
-
Pfam: clans, web tools and services
-
Finn R.D., Mistry J., Schuster-Bockler B., Griffiths-Jones S., Hollich V., Lassmann T., Moxon S., Marshall M., Khanna A., Durbin R., Eddy S.R., Sonnhammer E.L., and Bateman A. Pfam: clans, web tools and services. Nucleic Acids Res. 34 (2006) D247-D251
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Bockler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
Moxon, S.7
Marshall, M.8
Khanna, A.9
Durbin, R.10
Eddy, S.R.11
Sonnhammer, E.L.12
Bateman, A.13
-
30
-
-
85035250545
-
Measure representation and multifractal analysis of complete genomes
-
Yu Z.-G., Anh V., and Lau K.-S. Measure representation and multifractal analysis of complete genomes. Phys. Rev. E 64 (2001) 1-9
-
(2001)
Phys. Rev. E
, vol.64
, pp. 1-9
-
-
Yu, Z.-G.1
Anh, V.2
Lau, K.-S.3
-
31
-
-
84952321451
-
-
P. Deschavanne, A. Giron, J. Vilain, C. Dufraigne, B. Fertil, Genomic signature is preserved in short DNA fragments, in: BIBE2000 IEEE International Symposium on Bio-informatics & Biomedical engineering, Washington, USA, 8-10 November 2000, pp. 161-167.
-
P. Deschavanne, A. Giron, J. Vilain, C. Dufraigne, B. Fertil, Genomic signature is preserved in short DNA fragments, in: BIBE2000 IEEE International Symposium on Bio-informatics & Biomedical engineering, Washington, USA, 8-10 November 2000, pp. 161-167.
-
-
-
-
32
-
-
0034887748
-
Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier
-
Sandberg R., Winberg G., Bränden C.-I., Kaske A., Ernberg I., and Cöster J. Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier. Genome Res. 11 (2001) 1404-1409
-
(2001)
Genome Res.
, vol.11
, pp. 1404-1409
-
-
Sandberg, R.1
Winberg, G.2
Bränden, C.-I.3
Kaske, A.4
Ernberg, I.5
Cöster, J.6
-
33
-
-
33644876022
-
The PROSITE database
-
Hulo N., Bairoch A., Bulliard V., Cerutti L., De Castro E., Langendijk-Genevaux P.S., Pagni M., and Sigrist C.J.A. The PROSITE database. Nucleic Acids Res. 34 (2006) D227-D230
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Hulo, N.1
Bairoch, A.2
Bulliard, V.3
Cerutti, L.4
De Castro, E.5
Langendijk-Genevaux, P.S.6
Pagni, M.7
Sigrist, C.J.A.8
-
34
-
-
22144498433
-
Using supervised fuzzy clustering to predict protein structural classes
-
Shen H.B., Yang J., Liu X.J., and Chou K.C. Using supervised fuzzy clustering to predict protein structural classes. Biochem. Biophys. Res. Commun. 334 (2005) 577-581
-
(2005)
Biochem. Biophys. Res. Commun.
, vol.334
, pp. 577-581
-
-
Shen, H.B.1
Yang, J.2
Liu, X.J.3
Chou, K.C.4
-
35
-
-
2442592993
-
A hidden Markov model derived structural alphabet for proteins
-
Camproux A.C., Gautier R., and Tuffery P. A hidden Markov model derived structural alphabet for proteins. J. Mol. Biol. 339 (2004) 591-605
-
(2004)
J. Mol. Biol.
, vol.339
, pp. 591-605
-
-
Camproux, A.C.1
Gautier, R.2
Tuffery, P.3
-
36
-
-
2942601555
-
Support vector machines for predicting protein structural class
-
Cai Y.D., Liu X.J., Xu X., and Zhou G.P. Support vector machines for predicting protein structural class. BMC Bioinformatics 2 (2001) 1-5
-
(2001)
BMC Bioinformatics
, vol.2
, pp. 1-5
-
-
Cai, Y.D.1
Liu, X.J.2
Xu, X.3
Zhou, G.P.4
-
37
-
-
32644441676
-
Prediction of protein structural class with rough sets
-
Cao Y., Liu S., Zhang L., Qin J., Wang J., and Tang K. Prediction of protein structural class with rough sets. BMC Bioinformatics 7 (2006) 20-25
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 20-25
-
-
Cao, Y.1
Liu, S.2
Zhang, L.3
Qin, J.4
Wang, J.5
Tang, K.6
-
38
-
-
54749084166
-
An intriguing controversy over protein structural class prediction
-
Zhou G.P. An intriguing controversy over protein structural class prediction. J. Protein Chem. 17 (1998) 729-738
-
(1998)
J. Protein Chem.
, vol.17
, pp. 729-738
-
-
Zhou, G.P.1
|