-
3
-
-
0037250525
-
Improvements to CluSTr. the database of SWISS - PROT + TrEMBL protein clusters
-
Kriventseva E.V., Servant F., and Apweiler R. Improvements to CluSTr. the database of SWISS - PROT + TrEMBL protein clusters. Nucleic Acids Res. 31 (2003) 388-389
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 388-389
-
-
Kriventseva, E.V.1
Servant, F.2
Apweiler, R.3
-
5
-
-
0035175625
-
Proteome analysis database. online application of InterPro and CluSTr for the functional classification of proteins in whole genomes
-
Apweiler R., Biswas M., Fleischmann W., Kanapin A., Karavidopoulou Y., Kersey P., Kriventseva E.V., Mittard V., Mulder N., Phan I., and Zdobnov E. Proteome analysis database. online application of InterPro and CluSTr for the functional classification of proteins in whole genomes. Nucleic Acids Res. 29 (2001) 44-48
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 44-48
-
-
Apweiler, R.1
Biswas, M.2
Fleischmann, W.3
Kanapin, A.4
Karavidopoulou, Y.5
Kersey, P.6
Kriventseva, E.V.7
Mittard, V.8
Mulder, N.9
Phan, I.10
Zdobnov, E.11
-
6
-
-
0035072551
-
Clustering of highly homologous sequences to reduce the size of large protein databases
-
Li W., Jaroszewski L., and Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17 (2001) 282-283
-
(2001)
Bioinformatics
, vol.17
, pp. 282-283
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
7
-
-
0036699189
-
Sequence clustering strategies improve remote homology recognitions while reducing search times
-
Li W., Jaroszewski L., and Godzik A. Sequence clustering strategies improve remote homology recognitions while reducing search times. Protein Eng. 15 (2002) 643-649
-
(2002)
Protein Eng.
, vol.15
, pp. 643-649
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
8
-
-
0033965852
-
ProtoMap. automatic classification of protein sequences and hierarchy of protein families
-
Yona G., Linial N., and Linial M. ProtoMap. automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res. 28 (2000) 49-55
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 49-55
-
-
Yona, G.1
Linial, N.2
Linial, M.3
-
9
-
-
0037250523
-
ProtoNet. hierarchical classification of the protein space
-
Sasson O., Vaaknin A., Fleischer H., Portugaly E., Bilu Y., Linial N., and Linial M. ProtoNet. hierarchical classification of the protein space. Nucleic Acids Res. 31 (2003) 348-352
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 348-352
-
-
Sasson, O.1
Vaaknin, A.2
Fleischer, H.3
Portugaly, E.4
Bilu, Y.5
Linial, N.6
Linial, M.7
-
11
-
-
0036087099
-
SYSTERS, GeneNest, SpliceNest. exploring sequence space from genome to protein
-
Krause A., Haas S.A., Coward E., and Vingron M. SYSTERS, GeneNest, SpliceNest. exploring sequence space from genome to protein. Nucleic Acids Res. 30 (2002) 299-300
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 299-300
-
-
Krause, A.1
Haas, S.A.2
Coward, E.3
Vingron, M.4
-
12
-
-
8844286052
-
Incremental generation of summarized clustering hierarchy for protein family analysis
-
Chen C.-Y., Oyang Y.-J., and Juan H.-F. Incremental generation of summarized clustering hierarchy for protein family analysis. Bioinformatics 20 (2004) 2586-2596
-
(2004)
Bioinformatics
, vol.20
, pp. 2586-2596
-
-
Chen, C.-Y.1
Oyang, Y.-J.2
Juan, H.-F.3
-
13
-
-
0029559311
-
Sequence similarity analysis of Escherichia coli proteins-functional and evolutionary implications
-
Koonin E.V., Tatusov R.L., and Rudd K.E. Sequence similarity analysis of Escherichia coli proteins-functional and evolutionary implications. Proc. Natl. Acad. Sci. USA 92 (1995) 11921-11925
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 11921-11925
-
-
Koonin, E.V.1
Tatusov, R.L.2
Rudd, K.E.3
-
14
-
-
0029074668
-
A comprehensive representation of extensive similarity linkage between large numbers of proteins
-
Watanabe H., and Otsuka J. A comprehensive representation of extensive similarity linkage between large numbers of proteins. Comput. Appl. Biosci. 11 (1995) 159-166
-
(1995)
Comput. Appl. Biosci.
, vol.11
, pp. 159-166
-
-
Watanabe, H.1
Otsuka, J.2
-
15
-
-
0033944826
-
GeneRAGE: a robust algorithm for sequence clustering and domain detection
-
Enright A.J., and Ouzounis C.A. GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics 16 (2000) 451-457
-
(2000)
Bioinformatics
, vol.16
, pp. 451-457
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
16
-
-
0036327988
-
Clustering of proximal sequence space for the identification of protein families
-
Abascal F., and Valencia A. Clustering of proximal sequence space for the identification of protein families. Bioinformatics 18 (2002) 908-921
-
(2002)
Bioinformatics
, vol.18
, pp. 908-921
-
-
Abascal, F.1
Valencia, A.2
-
17
-
-
0001899680
-
The metric space of proteins. comparative study of clustering algorithms
-
Sasson O., Linial N., and Linial M. The metric space of proteins. comparative study of clustering algorithms. Bioinformatics 18 Suppl. 1 (2002) s14-s21
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Sasson, O.1
Linial, N.2
Linial, M.3
-
18
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright A.J., Dongen S.V., and Ouzounis C.A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30 (2002) 1575-1584
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Dongen, S.V.2
Ouzounis, C.A.3
-
19
-
-
0034777598
-
Clustering protein sequences-structure prediction by transitive homology
-
Bolten E., Schliep A., Schneckener S., Schomburg D., and Schrader R. Clustering protein sequences-structure prediction by transitive homology. Bioinformatics 17 (2001) 935-941
-
(2001)
Bioinformatics
, vol.17
, pp. 935-941
-
-
Bolten, E.1
Schliep, A.2
Schneckener, S.3
Schomburg, D.4
Schrader, R.5
-
20
-
-
1042292571
-
Graph-based clustering for finding distant relationships in a large set of protein sequences
-
Kawaji H., Takenaka Y., and Matsuda H. Graph-based clustering for finding distant relationships in a large set of protein sequences. Bioinformatics 20 (2004) 243-252
-
(2004)
Bioinformatics
, vol.20
, pp. 243-252
-
-
Kawaji, H.1
Takenaka, Y.2
Matsuda, H.3
-
21
-
-
0035748125
-
A graph-based clustering method for a large set of sequences using a graph partitioning algorithm
-
Kawaji H., Yamaguchi Y., Matsuda H., and Hashimoto A. A graph-based clustering method for a large set of sequences using a graph partitioning algorithm. Genome Inf. 12 (2001) 93-102
-
(2001)
Genome Inf.
, vol.12
, pp. 93-102
-
-
Kawaji, H.1
Yamaguchi, Y.2
Matsuda, H.3
Hashimoto, A.4
-
22
-
-
8844227627
-
A clustering method for molecular sequences based on pairwise similarity
-
Matsuda H., Ishihara T., and Hashimoto A. A clustering method for molecular sequences based on pairwise similarity. Genome Inf. 7 (1996) 23-32
-
(1996)
Genome Inf.
, vol.7
, pp. 23-32
-
-
Matsuda, H.1
Ishihara, T.2
Hashimoto, A.3
-
23
-
-
0032726692
-
ProtoMap. automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space
-
Yona G., Linial N., and Linial M. ProtoMap. automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins 37 (1999) 360-378
-
(1999)
Proteins
, vol.37
, pp. 360-378
-
-
Yona, G.1
Linial, N.2
Linial, M.3
-
24
-
-
0031876711
-
A set-theoretic approach to database searching and clustering
-
Krause A., and Vingron M. A set-theoretic approach to database searching and clustering. Bioinformatics 14 (1998) 430-438
-
(1998)
Bioinformatics
, vol.14
, pp. 430-438
-
-
Krause, A.1
Vingron, M.2
-
25
-
-
0346652457
-
ProClust. improved clustering of protein sequences with an extended graph-based approach
-
Pipenbacher P., Schliep A., Schneckener S., Schonhuth A., Schomburg D., and Schrader R. ProClust. improved clustering of protein sequences with an extended graph-based approach. Bioinformatics 18 Suppl. 2 (2002) s182-s191
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 2
-
-
Pipenbacher, P.1
Schliep, A.2
Schneckener, S.3
Schonhuth, A.4
Schomburg, D.5
Schrader, R.6
-
27
-
-
0016990971
-
The origin and evolution of protein superfamilies
-
Dayhoff M.O. The origin and evolution of protein superfamilies. Fed. Proc. 35 (1976) 2132-2138
-
(1976)
Fed. Proc.
, vol.35
, pp. 2132-2138
-
-
Dayhoff, M.O.1
-
28
-
-
0033597176
-
The relationship between protein structure and function. a comprehensive survey with application to the yeast genome
-
Hegyi H., and Gerstein M. The relationship between protein structure and function. a comprehensive survey with application to the yeast genome. J. Mol. Biol. 288 (1999) 147-164
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 147-164
-
-
Hegyi, H.1
Gerstein, M.2
-
29
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander C., and Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9 (1991) 56-68
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
30
-
-
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. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443-453
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
31
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith T.F., and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 14 (1981) 195-197
-
(1981)
J. Mol. Biol.
, vol.14
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
32
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85 (1988) 2444-2448
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
33
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 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
-
34
-
-
0030801002
-
Gapped BLAST and PSI-BLAST. a new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST. a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 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
-
35
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost B. Twilight zone of protein sequence alignments. Protein Eng. 12 (1999) 85-94
-
(1999)
Protein Eng.
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
36
-
-
0035022822
-
Limits of homology detection by pairwise sequence comparison
-
Spang R., and Vingron M. Limits of homology detection by pairwise sequence comparison. Bioinformatics 17 (2001) 338-342
-
(2001)
Bioinformatics
, vol.17
, pp. 338-342
-
-
Spang, R.1
Vingron, M.2
-
38
-
-
0029933671
-
Effective protein sequence comparison
-
Pearson W.R. Effective protein sequence comparison. Methods Enzymol 266 (1996) 227-258
-
(1996)
Methods Enzymol
, vol.266
, pp. 227-258
-
-
Pearson, W.R.1
-
39
-
-
0022906994
-
Implementing agglomerative hierarchic clustering algorithms for use in document retrieval
-
Voorhees E.M. Implementing agglomerative hierarchic clustering algorithms for use in document retrieval. Inf. Process. Manage. 22 6 (1986) 465-476
-
(1986)
Inf. Process. Manage.
, vol.22
, Issue.6
, pp. 465-476
-
-
Voorhees, E.M.1
-
40
-
-
0004161991
-
-
Prentice-Hall, Englewood Cliffs, NJ, USA
-
Jain A.K., and Dubes R.C. Algorithms for Clustering Data (1988), Prentice-Hall, Englewood Cliffs, NJ, USA
-
(1988)
Algorithms for Clustering Data
-
-
Jain, A.K.1
Dubes, R.C.2
-
41
-
-
0033957834
-
The Swiss-Prot protein sequence database and its supplement TrEmBL in 2000
-
Bairoch A., and Apweiler R. The Swiss-Prot protein sequence database and its supplement TrEmBL in 2000. Nucleic Acids Res. 28 (2000) 45-48
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 45-48
-
-
Bairoch, A.1
Apweiler, R.2
-
42
-
-
0034491031
-
InterPro-an integrated documentation resource for protein families, domains and functional sites
-
Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D.R., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J.A., and Zdobnov E.M. InterPro-an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16 (2000) 1145-1150
-
(2000)
Bioinformatics
, vol.16
, pp. 1145-1150
-
-
Apweiler, R.1
Attwood, T.K.2
Bairoch, A.3
Bateman, A.4
Birney, E.5
Biswas, M.6
Bucher, P.7
Cerutti, L.8
Corpet, F.9
Croning, M.D.R.10
Durbin, R.11
Falquet, L.12
Fleischmann, W.13
Gouzy, J.14
Hermjakob, H.15
Hulo, N.16
Jonassen, I.17
Kahn, D.18
Kanapin, A.19
Karavidopoulou, Y.20
Lopez, R.21
Marx, B.22
Mulder, N.J.23
Oinn, T.M.24
Pagni, M.25
Servant, F.26
Sigrist, C.J.A.27
Zdobnov, E.M.28
more..
-
45
-
-
0034786143
-
An automatic graph layout algorithm for similarity and network visualization
-
Enright A.J., and Ouzounis C.A. An automatic graph layout algorithm for similarity and network visualization. Bioinformatics 17 (2001) 853-854
-
(2001)
Bioinformatics
, vol.17
, pp. 853-854
-
-
Enright, A.J.1
Ouzounis, C.A.2
-
46
-
-
0033563350
-
Significance of Z-value statistics of Smith-Waterman scores for protein alignments
-
Comet J.P., Aude J.C., Glemet E., Risler J.L., Henaut A., Slonimski P.P., and Codani J.J. Significance of Z-value statistics of Smith-Waterman scores for protein alignments. Comput. Chem. 23 (1999) 317-331
-
(1999)
Comput. Chem.
, vol.23
, pp. 317-331
-
-
Comet, J.P.1
Aude, J.C.2
Glemet, E.3
Risler, J.L.4
Henaut, A.5
Slonimski, P.P.6
Codani, J.J.7
|