메뉴 건너뛰기




Volumn 259, Issue 4, 1996, Pages 840-854

FASTA-SWAP and FASTA-PAT: Pattern database searches using combinations of aligned amino acids, and a novel scoring theory

Author keywords

Amino acid sequence pattern; FASTA; Protein database search; Protein function identification; Scoring theory

Indexed keywords

AMINO ACID;

EID: 0030596506     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0362     Document Type: Article
Times cited : (12)

References (50)
  • 1
    • 0024988375 scopus 로고
    • Protein database searches for multiple alignments
    • Altschul, S. F. & Lipman, D. J. (1990). Protein database searches for multiple alignments. Proc. Natl Acad. Sci. USA, 87, 5509-5513.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 5509-5513
    • Altschul, S.F.1    Lipman, D.J.2
  • 3
    • 0028246722 scopus 로고
    • Prints - A protein motif fingerprint database
    • Attwood, T. K. & Beck, M. E. (1994). PRINTS - a protein motif fingerprint database. Protein Eng. 7, 841-848.
    • (1994) Protein Eng. , vol.7 , 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. Nucl. Acids Res. 20, 2013-2018.
    • (1992) Nucl. Acids Res. , vol.20 , pp. 2013-2018
    • Bairoch, A.1
  • 5
    • 0025303764 scopus 로고
    • Protein multiple sequence alignment and flexible pattern matching
    • Barton, G. J. (1990). Protein multiple sequence alignment and flexible pattern matching. Methods Enzymol. 183, 403-428.
    • (1990) Methods Enzymol. , vol.183 , pp. 403-428
    • Barton, G.J.1
  • 6
    • 0025275917 scopus 로고
    • Flexible protein sequence patterns. A sensitive method to detect weak structural similarities
    • Barton, G. J. & Sternberg, M. J. E. (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.E.2
  • 7
    • 0028502095 scopus 로고
    • Some useful properties of position-weight matrices
    • Claverie, J.-M. (1994). Some useful properties of position-weight matrices. Comput. Chem. 3, 287-294.
    • (1994) Comput. Chem. , vol.3 , pp. 287-294
    • Claverie, J.-M.1
  • 8
    • 0001282761 scopus 로고
    • Information enhancement methods for large scale sequence analysis
    • Claverie, J. M. & States, D. (1993). Information enhancement methods for large scale sequence analysis. Comput. Chemistry, 17, 191-202.
    • (1993) Comput. Chemistry , vol.17 , pp. 191-202
    • Claverie, J.M.1    States, D.2
  • 10
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff, M. O., ed, Natl Biomed. Res. Found., Washington, DC
    • Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. (1978). A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure (Dayhoff, M. O., ed), vol. 5, pp. 345-352, Natl Biomed. Res. Found., Washington, DC.
    • (1978) Atlas of Protein Sequence and Structure , vol.5 , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 12
    • 0028140271 scopus 로고
    • Fast protein block searches
    • Fuchs, R. (1994). Fast protein block searches. Comput. Appl. BioSci. 10, 79-80.
    • (1994) Comput. Appl. BioSci. , vol.10 , pp. 79-80
    • Fuchs, R.1
  • 13
    • 0011974253 scopus 로고
    • Genetics Computer Group, Inc., Madison, WI
    • Genetics Computer Group (1991). The GCG Package. Genetics Computer Group, Inc., Madison, WI.
    • (1991) The GCG Package
  • 15
    • 0026656815 scopus 로고
    • Exhaustive matching of the entire protein sequence database
    • Gonnet, G. H., Cohen, M. A. & Benner, S. (1993). Exhaustive matching of the entire protein sequence database. Science, 256, 1443-1445.
    • (1993) Science , vol.256 , pp. 1443-1445
    • Gonnet, G.H.1    Cohen, M.A.2    Benner, S.3
  • 16
    • 0028250468 scopus 로고
    • Profile analysis
    • Gribskov, M. (1994). Profile analysis. Methods Mol. Biol. 25, 247-266.
    • (1994) Methods Mol. Biol. , vol.25 , pp. 247-266
    • Gribskov, M.1
  • 17
  • 20
    • 0026410103 scopus 로고
    • Automated assembly of protein blocks for database searching
    • Henikoff, S. & Henikoff, J. G. (1991). Automated assembly of protein blocks for database searching. Nucl. Acids Res. 19, 6565-6572.
    • (1991) Nucl. Acids Res. , vol.19 , pp. 6565-6572
    • Henikoff, S.1    Henikoff, J.G.2
  • 21
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-105199.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 10915-105199
    • Henikoff, S.1    Henikoff, J.G.2
  • 22
    • 0028118434 scopus 로고
    • Protein family classification based on searching a database of blocks
    • Henikoff, S. & Henikoff, J. G. (1994a). 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
  • 23
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • Henikoff, S. & Henikoff, J. G. (1994b). 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
  • 24
    • 0027991446 scopus 로고
    • The FSSP database of structurally aligned protein fold families
    • Holm, L. & Sander, C. (1994). The FSSP database of structurally aligned protein fold families. Nucl. Acids Res. 22, 3600-3609.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 3600-3609
    • Holm, L.1    Sander, C.2
  • 25
    • 0028304908 scopus 로고
    • On global sequence alignment
    • Huang, X. (1994). On global sequence alignment. Comput. Applic. BioSci. 10, 227-235.
    • (1994) Comput. Applic. BioSci. , vol.10 , pp. 227-235
    • Huang, X.1
  • 26
    • 0027361123 scopus 로고
    • A structural basis for sequence comparisons. An evaluation of scoring methodologies
    • Johnson, M. S. & Overington, J. P. (1993). A structural basis for sequence comparisons. An evaluation of scoring methodologies. J. Mol. Biol. 223, 716-738.
    • (1993) J. Mol. Biol. , vol.223 , pp. 716-738
    • Johnson, M.S.1    Overington, J.P.2
  • 27
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Comput. Appl. BioSci. 8, 275-282.
    • (1992) Comput. Appl. Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 28
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin, S. & Altschul, S. F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA, 87, 2264-2268.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 29
    • 0001318108 scopus 로고
    • Statistical composition of high-scoring segments from molecular sequences
    • Karlin, S., Dembo, A. & Kawabata, T. (1990). Statistical composition of high-scoring segments from molecular sequences. Ann. Stat. 18, 571-581.
    • (1990) Ann. Stat. , vol.18 , pp. 571-581
    • Karlin, S.1    Dembo, A.2    Kawabata, T.3
  • 30
    • 0027081080 scopus 로고
    • ProSearch: Fast searching of protein sequences with regular expression patterns related to protein structure and function
    • Kolakowski, L. F., Leunissen, J. A. M. & Smith, J. E. (1992). ProSearch: fast searching of protein sequences with regular expression patterns related to protein structure and function. BioTechniques, 13, 919-921.
    • (1992) BioTechniques , vol.13 , pp. 919-921
    • Kolakowski, L.F.1    Leunissen, J.A.M.2    Smith, J.E.3
  • 31
    • 0028568602 scopus 로고
    • Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain - Study of a diverse, ancient protein superfamily using motif search and structural modeling
    • Koonin, E. V., Mushegian, A. R., Tatusov, R. L., Altschul, S. F., Bryant, S. H., Bork, P. & Valencia, A. (1994). Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain - study of a diverse, ancient protein superfamily using motif search and structural modeling. Protein Sci. 3, 2045-2054.
    • (1994) Protein Sci. , vol.3 , pp. 2045-2054
    • Koonin, E.V.1    Mushegian, A.R.2    Tatusov, R.L.3    Altschul, S.F.4    Bryant, S.H.5    Bork, P.6    Valencia, A.7
  • 32
    • 0028158905 scopus 로고
    • Improving the sensitivity of the sequence profile methods
    • Luthy, R., Xenarios, I. & Bucher, P. (1994). Improving the sensitivity of the sequence profile methods. Protein Sci. 3, 139-146.
    • (1994) Protein Sci. , vol.3 , pp. 139-146
    • Luthy, R.1    Xenarios, I.2    Bucher, P.3
  • 33
    • 0026511848 scopus 로고
    • A data bank merging related protein structures and sequences
    • Pascarella, S. & Argos, P. (1992). A data bank merging related protein structures and sequences. Protein Eng. 5, 121-137.
    • (1992) Protein Eng. , vol.5 , pp. 121-137
    • Pascarella, S.1    Argos, P.2
  • 34
    • 0025272240 scopus 로고
    • Rapid and sensitive sequence comparisons with FASTP and FASTA
    • Pearson, W. R. (1989). Rapid and sensitive sequence comparisons with FASTP and FASTA. Methods Enzymol. 183, 63-98.
    • (1989) Methods Enzymol. , vol.183 , pp. 63-98
    • Pearson, W.R.1
  • 35
  • 36
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 37
    • 0024604147 scopus 로고
    • Predicitive motifs derived from cytosine methyltransferases
    • Pösfai, J., Bhagwat, A. S., Pösfai, G. & Roberts, R. J. (1989). Predicitive motifs derived from cytosine methyltransferases. Nucl. Acids Res. 17, 2421-2437.
    • (1989) Nucl. Acids Res. , vol.17 , pp. 2421-2437
    • Pösfai, J.1    Bhagwat, A.S.2    Pösfai, G.3    Roberts, R.J.4
  • 38
    • 0011944541 scopus 로고
    • Weighting aligned protein or nucleic acid sequences to correct for unequal representation
    • Sibbald, P. R. & Argos, P. (1990). Weighting aligned protein or nucleic acid sequences to correct for unequal representation. J. Mol. Biol. 10, 19-29.
    • (1990) J. Mol. Biol. , vol.10 , pp. 19-29
    • Sibbald, P.R.1    Argos, P.2
  • 39
    • 0025141443 scopus 로고
    • Automatic generation of primary sequence patterns from sets of related protein sequences
    • Smith, R. F. & Smith, T. F. (1990). Automatic generation of primary sequence patterns from sets of related protein sequences. Proc. Natl Acad. Sci. USA, 87, 118-122.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 118-122
    • Smith, R.F.1    Smith, T.F.2
  • 40
    • 0026527758 scopus 로고
    • Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modeling
    • Smith, R. F. & Smith, T. F. (1992). Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modeling. Protein Eng. 5, 35-41.
    • (1992) Protein Eng. , vol.5 , pp. 35-41
    • Smith, R.F.1    Smith, T.F.2
  • 41
    • 0030013766 scopus 로고
    • BCM search Launcher - An integrated interface to molecular biology database search and analysis services available on the World-Wide Web
    • in the press
    • Smith, R. F., Wiese, B. A., Wojzinsky, M. K., Davison, D. B. & Worley, K. C. (1966). BCM Search Launcher - an integrated interface to molecular biology database search and analysis services available on the World-Wide Web. Genome Res. 6, in the press.
    • (1966) Genome Res. , vol.6
    • Smith, R.F.1    Wiese, B.A.2    Wojzinsky, M.K.3    Davison, D.B.4    Worley, K.C.5
  • 42
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T. F. & Waterman, M. S. (1981). Identification of common molecular subsequences. J. Mol. Biol. 13, 195-197.
    • (1981) J. Mol. Biol. , vol.13 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 43
    • 0028091659 scopus 로고
    • Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
    • Tatusov, R. L., Altschul, S. F. & Koonin, E. V. (1994). Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci. USA, 91, 12091-12095.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 12091-12095
    • Tatusov, R.L.1    Altschul, S.F.2    Koonin, E.V.3
  • 44
    • 0028013177 scopus 로고
    • Improved sensitivity of profile searches through the use of sequence weights and gap excision
    • Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994a). Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput. Appl. BioSci. 10, 19-29.
    • (1994) Comput. Appl. BioSci. , vol.10 , pp. 19-29
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 45
    • 0027968068 scopus 로고
    • CLUSTALW: Improving the sensitivity of progressive multiple alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994b). CLUSTALW: improving the sensitivity of progressive multiple alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucl. Acids Res. 22, 4673-4680.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 46
    • 0027496980 scopus 로고
    • Weighting in sequence sets: A comparison of methods in terms of generalized sequences
    • Vingron, M. & Sibbald, P. R. (1993. Weighting in sequence sets: a comparison of methods in terms of generalized sequences. Proc. Natl Acad. Sci. USA, 90, 8777-8781.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 8777-8781
    • Vingron, M.1    Sibbald, P.R.2
  • 47
    • 0026747032 scopus 로고
    • PATMAT: A searching and extraction program for sequence, pattern and block queries and databases
    • Wallace, J. C. & Henikoff, S. (1992). PATMAT: a searching and extraction program for sequence, pattern and block queries and databases. Comput. Applic. Biosci. 8, 249-254.
    • (1992) Comput. Applic. Biosci. , vol.8 , pp. 249-254
    • Wallace, J.C.1    Henikoff, S.2
  • 49
    • 0001514262 scopus 로고
    • Statistics of local complexity in amino acid sequences and sequence databases
    • Wootton, J. C. & Federhen, S. (1993). Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17, 149-164.
    • (1993) Comput. Chem. , vol.17 , pp. 149-164
    • Wootton, J.C.1    Federhen, S.2
  • 50
    • 0028835212 scopus 로고
    • BEAUTY: An enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results
    • Worley, K. C., Wiese, B. A. & Smith, R. F. (1995). BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results. Genome Res. 5, 173-184.
    • (1995) Genome Res. , vol.5 , pp. 173-184
    • Worley, K.C.1    Wiese, B.A.2    Smith, R.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.