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Volumn 32, Issue 4, 2004, Pages 1298-1307

LEON: Multiple alignment evaluation of neighbours

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 2542558960     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh294     Document Type: Article
Times cited : (24)

References (55)
  • 4
    • 0032085105 scopus 로고    scopus 로고
    • Protein annotation: Detective work for function prediction
    • Doerks,T., Bairoch,A. and Bork,P. (1998) Protein annotation: detective work for function prediction. Trends Genet., 14, 248-250.
    • (1998) Trends Genet. , vol.14 , pp. 248-250
    • Doerks, T.1    Bairoch, A.2    Bork, P.3
  • 5
    • 0033119399 scopus 로고    scopus 로고
    • Errors in genome annotation
    • Brenner,S.E. (1999) Errors in genome annotation. Trends Genet., 15, 132-133.
    • (1999) Trends Genet. , vol.15 , pp. 132-133
    • Brenner, S.E.1
  • 6
    • 0035838976 scopus 로고    scopus 로고
    • Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
    • Aloy,P., Querol,E., Aviles,F.X. and Sternberg,M.J. (2001) Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol., 311, 395-408.
    • (2001) J. Mol. Biol. , vol.311 , pp. 395-408
    • Aloy, P.1    Querol, E.2    Aviles, F.X.3    Sternberg, M.J.4
  • 7
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia,C. and Lesk,A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 8
    • 0033609902 scopus 로고    scopus 로고
    • Evolution of protein sequences and structures
    • Wood,T.C. and Pearson,W.R. (1999) Evolution of protein sequences and structures. J. Mol. Biol., 291, 977-995.
    • (1999) J. Mol. Biol. , vol.291 , pp. 977-995
    • Wood, T.C.1    Pearson, W.R.2
  • 9
    • 0034682894 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence
    • Yang,A.S. and Honig,B. (2000) An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. J. Mol. Biol., 301, 679-689.
    • (2000) J. Mol. Biol. , vol.301 , pp. 679-689
    • Yang, A.S.1    Honig, B.2
  • 10
    • 0036408311 scopus 로고    scopus 로고
    • Sequence variations within protein families are linearly related to structural variations
    • Koehl,P. and Levitt,M. (2002) Sequence variations within protein families are linearly related to structural variations. J. Mol. Biol., 323, 551-562.
    • (2002) J. Mol. Biol. , vol.323 , pp. 551-562
    • Koehl, P.1    Levitt, M.2
  • 11
    • 0034677669 scopus 로고    scopus 로고
    • Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
    • Wilson,C.A., Kreychman,J. and Gerstein,M. (2000) Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol., 297, 233-249.
    • (2000) J. Mol. Biol. , vol.297 , pp. 233-249
    • Wilson, C.A.1    Kreychman, J.2    Gerstein, M.3
  • 12
    • 0034767547 scopus 로고    scopus 로고
    • Annotation transfer for genomics: Measuring functional divergence in multi-domain proteins
    • Hegyi,H. and Gerstein,M. (2001) Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res., 11, 1632-1640.
    • (2001) Genome Res. , vol.11 , pp. 1632-1640
    • Hegyi, H.1    Gerstein, M.2
  • 13
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfarmlies, from a structural perspective
    • Todd,A.E., Orengo,C.A. and Thornton,J.M. (2001) Evolution of function in protein superfarmlies, from a structural perspective. J. Mol. Biol., 307, 1113-1143.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 14
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • Devos,D. and Valencia,A. (2001) Intrinsic errors in genome annotation. Trends Genet., 17, 429-431.
    • (2001) Trends Genet. , vol.17 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 15
    • 0036308741 scopus 로고    scopus 로고
    • Enzyme function less conserved than anticipated
    • Rost,B. (2002) Enzyme function less conserved than anticipated. J. Mol. Biol., 318, 595-608.
    • (2002) J. Mol. Biol. , vol.318 , pp. 595-608
    • Rost, B.1
  • 16
    • 0032229196 scopus 로고    scopus 로고
    • Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption
    • Galperin,M.Y. and Koonin,E.V. (1998) Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol., 1, 55-67.
    • (1998) In Silico Biol. , vol.1 , pp. 55-67
    • Galperin, M.Y.1    Koonin, E.V.2
  • 17
    • 0035972742 scopus 로고    scopus 로고
    • Multiple alignment of complete sequences (MACS) in the post-genomic era
    • Lecompte,O., Thompson,J.D., Plewniak,F., Thierry,J. and Poch,O. (2001) Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene, 270, 17-30.
    • (2001) Gene , vol.270 , pp. 17-30
    • Lecompte, O.1    Thompson, J.D.2    Plewniak, F.3    Thierry, J.4    Poch, O.5
  • 18
    • 0034255358 scopus 로고    scopus 로고
    • DbClustal: Rapid and reliable global multiple alignments of protein sequences detected by database searches
    • Thompson,J.D., Plewniak,F., Thierry,J. and Poch,O. (2000) DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches. Nucleic Acids Res., 28, 2919-2926.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2919-2926
    • Thompson, J.D.1    Plewniak, F.2    Thierry, J.3    Poch, O.4
  • 19
    • 0034623005 scopus 로고    scopus 로고
    • 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
  • 20
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh,K., Misawa,K., Kuma,K. and Miyata,T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30, 3059-3066.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 21
    • 0027764344 scopus 로고
    • Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
    • Livingstone,C.D. and Barton,G.J. (1993) Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput. Appl. Biosci., 9, 745-756.
    • (1993) Comput. Appl. Biosci. , vol.9 , pp. 745-756
    • Livingstone, C.D.1    Barton, G.J.2
  • 22
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: Calculation of positional conservation in a protein sequence alignment
    • Pei,J. and Grishin,N.V. (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17, 700-712.
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2
  • 23
    • 0037311804 scopus 로고    scopus 로고
    • SEGID: Identifying interesting segments in (multiple) sequence alignments
    • Wang,L. and Xu,Y. (2003) SEGID: identifying interesting segments in (multiple) sequence alignments. Bioinformatics, 19, 297-298.
    • (2003) Bioinformatics , vol.19 , pp. 297-298
    • Wang, L.1    Xu, Y.2
  • 24
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 25
    • 0036188264 scopus 로고    scopus 로고
    • Predicting reliable regions in protein sequence alignments
    • Cline,M., Hughey,R. and Karplus,K. (2002) Predicting reliable regions in protein sequence alignments. Bioinformatics, 18, 306-314.
    • (2002) Bioinformatics , vol.18 , pp. 306-314
    • Cline, M.1    Hughey, R.2    Karplus, K.3
  • 26
    • 0035824873 scopus 로고    scopus 로고
    • Towards a reliable objective function for multiple sequence alignments
    • Thompson,J.D., Plewniak,F., Ripp,R., Thierry,J.C. and Poch,O. (2001) Towards a reliable objective function for multiple sequence alignments. J. Mol. Biol., 314, 937-951.
    • (2001) J. Mol. Biol. , vol.314 , pp. 937-951
    • Thompson, J.D.1    Plewniak, F.2    Ripp, R.3    Thierry, J.C.4    Poch, O.5
  • 27
    • 0037339236 scopus 로고    scopus 로고
    • Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures
    • Errami,M., Geourjon,C. and Deleage,G. (2003) Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures. Bioinformatics, 19, 506-512.
    • (2003) Bioinformatics , vol.19 , pp. 506-512
    • Errami, M.1    Geourjon, C.2    Deleage, G.3
  • 28
    • 0041743084 scopus 로고    scopus 로고
    • Predicting reliable regions in protein alignments from sequence profiles
    • Tress,M.L., Jones,D. and Valencia,A. (2003) Predicting reliable regions in protein alignments from sequence profiles. J. Mol. Biol., 330, 705-718.
    • (2003) J. Mol. Biol. , vol.330 , pp. 705-718
    • Tress, M.L.1    Jones, D.2    Valencia, A.3
  • 29
    • 0034897827 scopus 로고    scopus 로고
    • Secator: A program for inferring protein subfamilies from phylogenetic trees
    • Wicker,N., Perrin,G.R., Thierry,J.C. and Poch,O. (2001) Secator: a program for inferring protein subfamilies from phylogenetic trees. Mol. Biol. Evol., 18, 1435-1441.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1435-1441
    • Wicker, N.1    Perrin, G.R.2    Thierry, J.C.3    Poch, O.4
  • 30
    • 0038391401 scopus 로고    scopus 로고
    • RASCAL: Rapid scanning and correction of multiple sequence alignments
    • Thompson,J.D., Thierry,J.C. and Poch,O. (2003) RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics, 19, 1155-1161.
    • (2003) Bioinformatics , vol.19 , pp. 1155-1161
    • Thompson, J.D.1    Thierry, J.C.2    Poch, O.3
  • 31
    • 0031576361 scopus 로고    scopus 로고
    • Intermediate sequences increase the detection of homology between sequences
    • Park,J., Teichmann,S.A., Hubbard,T. and Chothia,C. (1997) Intermediate sequences increase the detection of homology between sequences. J. Mol. Biol., 273, 349-354.
    • (1997) J. Mol. Biol. , vol.273 , pp. 349-354
    • Park, J.1    Teichmann, S.A.2    Hubbard, T.3    Chothia, C.4
  • 32
    • 0032940341 scopus 로고    scopus 로고
    • Combining sensitive database searches with multiple intermediates to detect distant homologues
    • Salamov,A.A., Suwa,M., Orengo,C.A. and Swindells,M.B. (1999) Combining sensitive database searches with multiple intermediates to detect distant homologues. Protein Eng., 12, 95-100.
    • (1999) Protein Eng. , vol.12 , pp. 95-100
    • Salamov, A.A.1    Suwa, M.2    Orengo, C.A.3    Swindells, M.B.4
  • 34
  • 35
  • 36
    • 0022510143 scopus 로고
    • Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins
    • Engelman,D.M., Steitz,T.A. and Goldman,A. (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem., 15, 321-353.
    • (1986) Annu. Rev. Biophys. Biophys. Chem. , vol.15 , pp. 321-353
    • Engelman, D.M.1    Steitz, T.A.2    Goldman, A.3
  • 37
    • 0026356891 scopus 로고
    • Predicting coiled coils from protein sequences
    • Lupas,A., Van,D.M. and Stock,J. (1991) Predicting coiled coils from protein sequences. Science, 252, 1162-1164.
    • (1991) Science , vol.252 , pp. 1162-1164
    • Lupas, A.1    Van, D.M.2    Stock, J.3
  • 38
    • 0001514262 scopus 로고
    • Statistics of local complexity in amino acid sequences and sequence databases
    • Wootton,J. and Federhen,S. (1993) Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem., 17, 149-163.
    • (1993) Comput. Chem. , vol.17 , pp. 149-163
    • Wootton, J.1    Federhen, S.2
  • 43
    • 24544454670 scopus 로고    scopus 로고
    • Analyse statistique des structures tridimensionelles de proteines et validation de familles structurales a has taux d'identite
    • PhD Thesis: Universite Claude Bernard Lyon 1
    • Errami,M. PhD Thesis: Analyse statistique des structures tridimensionelles de proteines et validation de familles structurales a has taux d'identite. Universite Claude Bernard Lyon 1.
    • Errami, M.1
  • 44
  • 47
    • 0026656815 scopus 로고
    • Exhaustive matching of the entire protein sequence database
    • Gonnet,G.H., Cohen,M.A. and Benner,S.A. (1992) Exhaustive matching of the entire protein sequence database. Science, 256, 1443-1445.
    • (1992) Science , vol.256 , pp. 1443-1445
    • Gonnet, G.H.1    Cohen, M.A.2    Benner, S.A.3
  • 48
    • 0027968068 scopus 로고
    • 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
  • 50
    • 0028838717 scopus 로고
    • Threading a database of protein cores
    • Madej,T., Gibrat,J.F. and Bryant,S.H. (1995) Threading a database of protein cores. Proteins, 23, 356-369.
    • (1995) Proteins , vol.23 , pp. 356-369
    • Madej, T.1    Gibrat, J.F.2    Bryant, S.H.3
  • 51
    • 0024039650 scopus 로고
    • Sequence and nitrate regulation of the Arabidopsis thaliana mRNA encoding nitrate reductase, a metalloflavoprotein with three functional domains
    • Crawford,N.M., Smith,M., Bellissimo,D. and Davis,R.W. (1988) Sequence and nitrate regulation of the Arabidopsis thaliana mRNA encoding nitrate reductase, a metalloflavoprotein with three functional domains. Proc. Natl Acad. Sci. USA, 85, 5006-5010.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 5006-5010
    • Crawford, N.M.1    Smith, M.2    Bellissimo, D.3    Davis, R.W.4
  • 53
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3


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