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Volumn 12, Issue 2, 1996, Pages 135-143

Using substitution probabilities to improve position-specific scoring matrices

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

EID: 0029977162     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/12.2.135     Document Type: Article
Times cited : (151)

References (33)
  • 2
    • 0025878149 scopus 로고
    • 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, 555-565.
    • (1991) J. Mol. Biol. , vol.219 , pp. 555-565
    • Altschul, S.F.1
  • 3
    • 0028246722 scopus 로고
    • PRINTS-a protein motif fingerprint database
    • Attwood.T.K. and Beck, M.E. (1994) PRINTS-a protein motif fingerprint database. Protein Eng., 1, 841-848.
    • (1994) Protein Eng , vol.1 , pp. 841-848
    • Attwood, T.K.1    Beck, M.E.2
  • 4
    • 0026553672 scopus 로고
    • PROSITE: A dictionary of sites and patterns in proteins
    • Bairoch.A. (1992) PROSITE: A dictionary of sites and patterns in proteins. Nucleic Acids Res., 20, 2013-2018.
    • (1992) Nucleic Acids Res , vol.20 , pp. 2013-2018
    • Bairoch, A.1
  • 5
    • 0026562263 scopus 로고
    • The SWISS-PROT protein sequence data bank
    • Bairoch, A. and Boeckmann, B. (1992) The SWISS-PROT protein sequence data bank. Nucleic Acids Res., 20, 2019-2022.
    • (1992) Nucleic Acids Res , vol.20 , pp. 2019-2022
    • Bairoch, A.1    Boeckmann, B.2
  • 6
    • 0025275917 scopus 로고
    • Flexible protein sequence patterns. A sensitive method to detect weak structural similarities
    • Barton.G.J. and Sternberg, M.J. (1990) Flexible protein sequence patterns. A sensitive method to detect weak structural similarities. J. Mol. Biol., 212, 389-402.
    • (1990) J. Mol. Biol. , vol.212 , pp. 389-402
    • Barton, G.J.1    Sternberg, M.J.2
  • 9
    • 0028502095 scopus 로고
    • Some useful statistical properties of position-weight matrices
    • Claverie, J.-M. (1994) Some useful statistical properties of position-weight matrices. Comput. Chent., 18, 287-293.
    • (1994) Comput. Chent. , vol.18 , pp. 287-293
    • Claverie, J.-M.1
  • 10
    • 0000228203 scopus 로고
    • National Biomedical Research Foundation, Washington, DC, pp
    • Dayhoff, M. (1978) Atlas of protein sequence and structure., vol. 5, suppl. 3. National Biomedical Research Foundation, Washington, DC, pp. 345-358.
    • (1978) Atlas of Protein Sequence and Structure , vol.5 , pp. 345-358
    • Dayhoff, M.1
  • 11
    • 0023644680 scopus 로고
    • Systematic method for the detection of potential lambda Cro-like DNA-binding regions in proteins
    • Dodd.I.B. and Egan.J.B. (1987) Systematic method for the detection of potential lambda Cro-like DNA-binding regions in proteins. J. Mol. Biol., 194, 557-564.
    • (1987) J. Mol. Biol. , vol.194 , pp. 557-564
    • Dodd, I.B.1    Egan, J.B.2
  • 12
    • 0028360556 scopus 로고
    • Ancient conserved regions in gene sequences
    • Green, P. (1994) Ancient conserved regions in gene sequences. Curr. Opin. Struct. Biol., 4, 404-412.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 404-412
    • Green, P.1
  • 14
    • 0026410103 scopus 로고
    • Automated assembly of protein blocks for database searching
    • Henikoff, S. and Henikoff.J.G. (1991) Automated assembly of protein blocks for database searching. Nucleic Acids Res., 19, 6565-6572.
    • (1991) Nucleic Acids Res , vol.19 , pp. 6565-6572
    • Henikoff, S.1    Henikoff, J.G.2
  • 15
    • 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
  • 16
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • Henikoff.S. and Henikoff, J.G. (1994a) Position-based sequence weights. J. Mol. Biol., 243, 574-578.
    • (1994) J. Mol. Biol. , vol.243 , pp. 574-578
    • Henikoff, S.1    Henikoff, J.G.2
  • 17
    • 0028118434 scopus 로고
    • Protein family classification based on searching a database of blocks
    • Henikoff, S. and Henikoff, J.G. (1994b) Protein family classification based on searching a database of blocks. Genomics, 19, 97-107.
    • (1994) Genomics , vol.19 , pp. 97-107
    • Henikoff, S.1    Henikoff, J.G.2
  • 18
    • 0025371704 scopus 로고
    • Finding protein similarities with nucleotide sequence databases
    • Henikoff.S., Wallace.J.C. and Brown.J.P. (1990) Finding protein similarities with nucleotide sequence databases. Methods Enzymoi, 183, 111-132.
    • (1990) Methods Enzymoi , vol.183 , pp. 111-132
    • Henikoff, S.1    Wallace, J.C.2    Brown, J.P.3
  • 19
    • 0028825276 scopus 로고
    • Automated construction and graphical presentation of protein blocks from unaligned sequences
    • Henikoff.S., Henikoff, J.G., Alford, W.J. and Pietrokovski, S. (1995) Automated construction and graphical presentation of protein blocks from unaligned sequences. Gene, 163, GC17—GC26.
    • (1995) Gene , vol.163 , pp. GC17-GC26
    • Henikoff, S.1    Henikoff, J.G.2    Alford, W.J.3    Pietrokovski, S.4
  • 20
    • 0028105794 scopus 로고
    • Yeast chromosome III: New gene families
    • Koonin.E.V., Bork.P. and Sander.C. (1994) Yeast chromosome III: new gene families. EMBO J., 13, 493-503.
    • (1994) EMBO J , vol.13 , pp. 493-503
    • Koonin, E.V.1    Bork, P.2    Sander, C.3
  • 22
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence.C.E., Altschul, S.F., Boguski.M.S., Liu.J.S. Neuwald.A.F., and Wootton.J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208—214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 23
    • 0028158905 scopus 로고
    • Improving the sensitivity of the sequence profile method
    • Liithy.R., Xenarios, I. and Bucher.P. (1994) Improving the sensitivity of the sequence profile method. Prot. Sci., 3, 139-146.
    • (1994) Prot. Sci. , vol.3 , pp. 139-146
    • Liithy, R.1    Xenarios, I.2    Bucher, P.3
  • 24
    • 0018079655 scopus 로고
    • Basic principles of ROC analysis
    • Metz, C.E. (1978) Basic principles of ROC analysis. Sem. Nuclear Med., 8, 283-298.
    • (1978) Sem. Nuclear Med. , vol.8 , pp. 283-298
    • Metz, C.E.1
  • 26
    • 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
  • 27
    • 0029006770 scopus 로고
    • Comparison of methods for searching protein sequence databases
    • Pearson, W.R. (1995) Comparison of methods for searching protein sequence databases. Prot. Sci., 4, 1145-1160.
    • (1995) Prot. Sci. , vol.4 , pp. 1145-1160
    • Pearson, W.R.1
  • 28
    • 0025017156 scopus 로고
    • Finding sequence motifs in groups of functionally related proteins
    • Smith, H.O., Annau.T.M. and Chandrasegaran, S. (1990) Finding sequence motifs in groups of functionally related proteins. Proc. Natl Acad. Sci. USA, 87, 826-830.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 826-830
    • Smith, H.O.1    Annau, T.M.2    Chandrasegaran, S.3
  • 29
    • 0028218683 scopus 로고
    • Modular arrangement of proteins as inferred from analysis of homology
    • Sonnhammer, E.L.L. and Kahn, D. (1994) Modular arrangement of proteins as inferred from analysis of homology. Prot. Sci., 3, 482-492.
    • (1994) Prot. Sci. , vol.3 , pp. 482-492
    • Sonnhammer, E.L.L.1    Kahn, D.2
  • 30
    • 0025342573 scopus 로고
    • Consensus patterns in DNA
    • Stormo, G.D. (1990) Consensus patterns in DNA. Methods Enzymoi., 183, 211-221.
    • (1990) Methods Enzymoi , vol.183 , pp. 211-221
    • Stormo, G.D.1
  • 31
    • 0028091659 scopus 로고
    • Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
    • Tatusov, R.L., Altschul.S.F. and Koonin.E.V. (1994) Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Nail Acad. Sci. USA, 91, 12091-12095.
    • (1994) Proc. Nail Acad. Sci. USA , vol.91 , pp. 12091-12095
    • Tatusov, R.L.1    Altschul, S.F.2    Koonin, E.V.3
  • 32
    • 0028013177 scopus 로고
    • Improved sensitivity of profile searches through the use of sequence weights and gap excision
    • Thompson.J.D., Higgins, D.G. and Gibson.T.J. (1994) Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Applic. Biosci., 10, 19-29.
    • (1994) Comput. Applic. Biosci. , vol.10 , pp. 19-29
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 33
    • 0024544755 scopus 로고
    • A fast and sensitive multiple sequence alignment algorithm
    • Vingron, M. and Argos, P. (1989) A fast and sensitive multiple sequence alignment algorithm. Comput. Applic. Biosci., 5, 115-121.
    • (1989) Comput. Applic. Biosci. , vol.5 , pp. 115-121
    • Vingron, M.1    Argos, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.