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Volumn 30, Issue 3, 2014, Pages 317-325

Revisiting amino acid substitution matrices for identifying distantly related proteins

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; METHODOLOGY; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

EID: 84893325672     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt694     Document Type: Article
Times cited : (32)

References (44)
  • 1
    • 84878792870 scopus 로고    scopus 로고
    • The parasite specific substitution matrices improve the annotation of apicomplexan proteins
    • Ali, J., et al. (2012) The parasite specific substitution matrices improve the annotation of apicomplexan proteins. BMC Genomics, 13 (Suppl. 7) , S19.
    • (2012) BMC Genomics , vol.13 , Issue.SUPPL. 7
    • Ali, J.1
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S.F., et al. (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
  • 3
    • 38549153238 scopus 로고    scopus 로고
    • Data growth and its impact on the SCOP database: New developments
    • Andreeva, A., et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, D419-D425.
    • (2008) Nucleic Acids Res , vol.36
    • Andreeva, A.1
  • 4
    • 84870779164 scopus 로고    scopus 로고
    • Discriminative modelling of context-specific amino acid substitution probabilities
    • Angermuller, C., et al. (2012) Discriminative modelling of context-specific amino acid substitution probabilities. Bioinformatics, 28, 3240-3247.
    • (2012) Bioinformatics , vol.28 , pp. 3240-3247
    • Angermuller, C.1
  • 5
    • 0028092214 scopus 로고
    • Amino acid substitution during functionally constrained divergent evolution of protein sequences
    • Benner, S.A., et al. (1994) Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng., 7, 1323-1332.
    • (1994) Protein Eng , vol.7 , pp. 1323-1332
    • Benner, S.A.1
  • 6
    • 62649147821 scopus 로고    scopus 로고
    • Sequence context-specific profiles for homology searching
    • Biegert, A. and Soding, J. (2009) Sequence context-specific profiles for homology searching. Proc. Natl Acad. Sci. USA, 106, 3770-3775.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 3770-3775
    • Biegert, A.1    Soding, J.2
  • 7
    • 44649194987 scopus 로고    scopus 로고
    • A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins
    • Brick, K. and Pizzi, E. (2008) A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins. BMC Bioinformatics, 9, 236.
    • (2008) BMC Bioinformatics , vol.9 , pp. 236
    • Brick, K.1    Pizzi, E.2
  • 8
    • 0348129526 scopus 로고    scopus 로고
    • The ASTRAL compendium in 2004
    • Chandonia, J.-M., et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32, D189-D192.
    • (2004) Nucleic Acids Res , vol.32
    • Chandonia, J.-M.1
  • 9
    • 27544499548 scopus 로고    scopus 로고
    • Pairwise alignment incorporating dipeptide covariation
    • Crooks, G.E., et al. (2005) Pairwise alignment incorporating dipeptide covariation. Bioinformatics, 21, 3704-3710.
    • (2005) Bioinformatics , vol.21 , pp. 3704-3710
    • Crooks, G.E.1
  • 10
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff, M.O., et al. (1978) A model of evolutionary change in proteins. Atlas Protein Seq. Strut., 5, 345-352.
    • (1978) Atlas Protein Seq. Strut , vol.5 , pp. 345-352
    • Dayhoff, M.O.1
  • 11
    • 0036017382 scopus 로고    scopus 로고
    • RtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
    • Dimmic, M.W., et al. (2002) rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J. Mol. Evol., 55, 65-73.
    • (2002) J. Mol. Evol , vol.55 , pp. 65-73
    • Dimmic, M.W.1
  • 12
    • 72549111108 scopus 로고    scopus 로고
    • Optimizing substitution matrix choice and gap parameters for sequence alignment
    • Edgar, R.C. (2009) Optimizing substitution matrix choice and gap parameters for sequence alignment. BMC Bioinformatics, 10, 396.
    • (2009) BMC Bioinformatics , vol.10 , pp. 396
    • Edgar, R.C.1
  • 13
    • 84870431038 scopus 로고    scopus 로고
    • CD-HIT: Accelerated for clustering the next-generation sequencing data
    • Fu, L., et al. (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28, 3150-3152.
    • (2012) Bioinformatics , vol.28 , pp. 3150-3152
    • Fu, L.1
  • 14
    • 12144279008 scopus 로고    scopus 로고
    • Contextual alignment of biological sequences (Extended abstract)
    • Gambin, A., et al. (2002) Contextual alignment of biological sequences (Extended abstract) . Bioinformatics, 18 (Suppl. 2) , S116-S127.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 2
    • Gambin, A.1
  • 15
    • 0028279408 scopus 로고
    • Analysis of amino acid substitution during divergent evolution: The 400 by 400 dipeptide substitution matrix
    • Gonnet, G.H., et al. (1994) Analysis of amino acid substitution during divergent evolution: the 400 by 400 dipeptide substitution matrix. Biochem. Biophys. Res. Commun., 199, 489-496.
    • (1994) Biochem. Biophys. Res. Commun , vol.199 , pp. 489-496
    • Gonnet, G.H.1
  • 16
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough, J., et al. (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J.Mol. Biol., 313, 903-919.
    • (2001) J.Mol. Biol , vol.313 , pp. 903-919
    • Gough, J.1
  • 17
    • 0345983651 scopus 로고    scopus 로고
    • Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison
    • Green, R.E. and Brenner, S.E. (2002) Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison. Proc. IEEE, 90, 1834-1847.
    • (2002) Proc. IEEE , vol.90 , pp. 1834-1847
    • Green, R.E.1    Brenner, S.E.2
  • 18
    • 0001969211 scopus 로고    scopus 로고
    • Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
    • Gribskov, M. and Robinson, N.L. (1996) Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem., 20, 25-33.
    • (1996) Comput. Chem , vol.20 , pp. 25-33
    • Gribskov, M.1    Robinson, N.L.2
  • 19
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. and Henikoff, J.G. (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
  • 20
    • 56649103902 scopus 로고    scopus 로고
    • Searching protein structure databases with DaliLite v.3
    • Holm, L., et al (2008) Searching protein structure databases with DaliLite v.3. Bioinformatics, 24, 2780-2781.
    • (2008) Bioinformatics , vol.24 , pp. 2780-2781
    • Holm, L.1
  • 21
    • 2342428875 scopus 로고    scopus 로고
    • Optimizing substitution matrices by separating score distributions
    • Hourai, Y., et al. (2004) Optimizing substitution matrices by separating score distributions. Bioinformatics, 20, 863-873.
    • (2004) Bioinformatics , vol.20 , pp. 863-873
    • Hourai, Y.1
  • 22
    • 32544461476 scopus 로고    scopus 로고
    • Improved pairwise alignments of proteins in the twilight zone using local structure predictions
    • Huang, Y.M. and Bystroff, C. (2006) Improved pairwise alignments of proteins in the twilight zone using local structure predictions. Bioinformatics, 22, 413-422.
    • (2006) Bioinformatics , vol.22 , pp. 413-422
    • Huang, Y.M.1    Bystroff, C.2
  • 23
    • 84856241300 scopus 로고    scopus 로고
    • Pattern of amino acid substitutions in transmembrane domains of beta-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria
    • Jimenez-Morales, D. and Liang, J. (2011) Pattern of amino acid substitutions in transmembrane domains of beta-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria. PLoS One, 6, e26400.
    • (2011) PLoS One , vol.6
    • Jimenez-Morales, D.1    Liang, J.2
  • 24
    • 61849149241 scopus 로고    scopus 로고
    • Detecting remote homologues using scoring matrices calculated from the estimation of amino acid substitution rates of beta-barrel membrane proteins
    • Jimenez-Morales, D., et al. (2008) Detecting remote homologues using scoring matrices calculated from the estimation of amino acid substitution rates of beta-barrel membrane proteins. Conf. Proc. IEEE Eng. Med. Biol. Soc., 2008, 1347-1350.
    • (2008) Conf. Proc. IEEE Eng. Med. Biol. Soc , vol.2008 , pp. 1347-1350
    • Jimenez-Morales, D.1
  • 25
    • 0033842326 scopus 로고    scopus 로고
    • Use of residue pairs in protein sequence-sequence and sequence-structure alignments
    • Jung, J. and Lee, B. (2000) Use of residue pairs in protein sequence-sequence and sequence-structure alignments. Protein Sci., 9, 1576-1588.
    • (2000) Protein Sci , vol.9 , pp. 1576-1588
    • Jung, J.1    Lee, B.2
  • 26
    • 0034562066 scopus 로고    scopus 로고
    • Optimization of a new score function for the detection of remote homologs
    • Kann, M., et al. (2000) Optimization of a new score function for the detection of remote homologs. Proteins, 41, 498-503.
    • (2000) Proteins , vol.41 , pp. 498-503
    • Kann, M.1
  • 27
    • 80051636221 scopus 로고    scopus 로고
    • Protein sequence alignment with family-specific amino acid similarity matrices
    • Kuznetsov, I.B. (2011) Protein sequence alignment with family-specific amino acid similarity matrices. BMC Res. Notes, 4, 296.
    • (2011) BMC Res. Notes , vol.4 , pp. 296
    • Kuznetsov, I.B.1
  • 28
    • 44349084889 scopus 로고    scopus 로고
    • Simple is beautiful: A straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches
    • Lee, M.M., et al. (2008) Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches. Bioinformatics, 24, 1339-1343.
    • (2008) Bioinformatics , vol.24 , pp. 1339-1343
    • Lee, M.M.1
  • 29
    • 82055171939 scopus 로고    scopus 로고
    • A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships
    • Lemaitre, C., et al. (2011) A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships. BMC Bioinformatics, 12, 457.
    • (2011) BMC Bioinformatics , vol.12 , pp. 457
    • Lemaitre, C.1
  • 30
    • 84876525081 scopus 로고    scopus 로고
    • Genome3D: A UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
    • Lewis, T.E., et al. (2013) Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res., 41, D499-D507.
    • (2013) Nucleic Acids Res , vol.41
    • Lewis, T.E.1
  • 31
    • 78650009547 scopus 로고    scopus 로고
    • Substitution matrices of residue triplets derived from protein blocks
    • Liu, X. and Zhao, Y.P. (2010) Substitution matrices of residue triplets derived from protein blocks. J. Comput. Biol., 17, 1679-1687.
    • (2010) J. Comput. Biol , vol.17 , pp. 1679-1687
    • Liu, X.1    Zhao, Y.P.2
  • 32
    • 0035230037 scopus 로고    scopus 로고
    • Non-symmetric score matrices and the detection of homologous transmembrane proteins
    • Muller, T., et al. (2001) Non-symmetric score matrices and the detection of homologous transmembrane proteins. Bioinformatics, 17 (Suppl. 1) , S182-S189.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Muller, T.1
  • 33
    • 0036134748 scopus 로고    scopus 로고
    • Estimating amino acid substitution models: A comparison of Dayhoffs estimator, the resolvent approach and a maximum likelihood method
    • Muller, T., et al. (2002) Estimating amino acid substitution models: a comparison of Dayhoffs estimator, the resolvent approach and a maximum likelihood method. Mol. Biol. Evol., 19, 8-13.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 8-13
    • Muller, T.1
  • 34
    • 0033670313 scopus 로고    scopus 로고
    • PHAT: A transmembrane-specific substitution matrix Predicted hydrophobic and transmembrane
    • Ng, P.C., et al. (2000) PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics, 16, 760-766.
    • (2000) Bioinformatics , vol.16 , pp. 760-766
    • Ng, P.C.1
  • 35
    • 58649097284 scopus 로고    scopus 로고
    • Fr-TM-align: A new protein structural alignment method based on fragment alignments and the TM-score
    • Pandit, S.B. and Skolnick, J. (2008) Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinformatics, 9, 531.
    • (2008) BMC Bioinformatics , vol.9 , pp. 531
    • Pandit, S.B.1    Skolnick, J.2
  • 36
    • 0025950944 scopus 로고
    • 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
  • 37
    • 0036721466 scopus 로고    scopus 로고
    • Optimization of a new score function for the generation of accurate alignments
    • Qian, B. and Goldstein, R.A. (2002) Optimization of a new score function for the generation of accurate alignments. Proteins, 48, 605-610.
    • (2002) Proteins , vol.48 , pp. 605-610
    • Qian, B.1    Goldstein, R.A.2
  • 38
    • 84907095419 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • Vienna, Austria
    • R Development Core Team. (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
    • (2012) R Foundation for Statistical Computing
  • 39
    • 33746329568 scopus 로고    scopus 로고
    • Optimizing amino acid substitution matrices with a local alignment kernel
    • Saigo, H., et al. (2006) Optimizing amino acid substitution matrices with a local alignment kernel. BMC Bioinformatics, 7, 246.
    • (2006) BMC Bioinformatics , vol.7 , pp. 246
    • Saigo, H.1
  • 40
    • 0035878724 scopus 로고    scopus 로고
    • Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
    • Schaffer, A.A., et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res., 29, 2994-3005.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2994-3005
    • Schaffer, A.A.1
  • 41
    • 84876578144 scopus 로고    scopus 로고
    • New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures
    • Sillitoe, I., et al. (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res., 41, D490-D498.
    • (2013) Nucleic Acids Res , vol.41
    • Sillitoe, I.1
  • 42
    • 0029922443 scopus 로고    scopus 로고
    • Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
    • Tomii, K. and Kanehisa, M. (1996) Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng., 9, 27-36.
    • (1996) Protein Eng , vol.9 , pp. 27-36
    • Tomii, K.1    Kanehisa, M.2
  • 43
    • 0028047892 scopus 로고
    • Sequence alignment and penalty choice. Review of concepts, case studies and implications
    • Vingron, M. and Waterman, M.S. (1994) Sequence alignment and penalty choice. Review of concepts, case studies and implications. J. Mol. Biol., 235, 1-12.
    • (1994) J. Mol. Biol , vol.235 , pp. 1-12
    • Vingron, M.1    Waterman, M.S.2
  • 44
    • 0346734129 scopus 로고    scopus 로고
    • The compositional adjustment of amino acid substitution matrices
    • Yu, Y.K., et al. (2003) The compositional adjustment of amino acid substitution matrices. Proc. Natl Acad. Sci. USA, 100, 15688-15693.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 15688-15693
    • Yu, Y.K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.