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Volumn 24, Issue 11, 2008, Pages 1339-1343

Simple is beautiful: A straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; FALSE POSITIVE RESULT; GENETIC DATABASE; INFORMATION RETRIEVAL; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY;

EID: 44349084889     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn130     Document Type: Article
Times cited : (21)

References (32)
  • 1
    • 4644269503 scopus 로고    scopus 로고
    • Comparative homology agreements earch: An effective combination of homology-search methods
    • Alam,I. et al. (2004) Comparative homology agreements earch: An effective combination of homology-search methods. Proc. Natl. Acad. Sci USA, 101, 13814-13819.
    • (2004) Proc. Natl. Acad. Sci USA , vol.101 , pp. 13814-13819
    • Alam, I.1
  • 2
    • 0029889221 scopus 로고    scopus 로고
    • Local alignment statistics
    • Altschul,S.F. and Gish,W. (1996) Local alignment statistics. Methods Enzymol. 266, 460-480.
    • (1996) Methods Enzymol , vol.266 , pp. 460-480
    • Altschul, S.F.1    Gish, W.2
  • 3
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
    • (1990) J. Mol. Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1
  • 4
    • 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
  • 5
    • 0033574503 scopus 로고    scopus 로고
    • Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches
    • Aravind,L. and Koonin,E.V. (1999) Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Bio., 287, 1023-1040.
    • (1999) J. Mol. Bio , vol.287 , pp. 1023-1040
    • Aravind, L.1    Koonin, E.V.2
  • 6
    • 2942511670 scopus 로고    scopus 로고
    • PubMatrix: A tool for multiplex literature mining
    • Becker,K.G. et al. (2003) PubMatrix: A tool for multiplex literature mining. BMC Bioinformatics, 4, 61.
    • (2003) BMC Bioinformatics , vol.4 , pp. 61
    • Becker, K.G.1
  • 7
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie,J.U. et al. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-253.
    • (1991) Science , vol.253 , pp. 164-253
    • Bowie, J.U.1
  • 8
    • 0029948769 scopus 로고    scopus 로고
    • Three-dimensional profiles for measuring compatibility of amino acid sequence with three-dimensional structure
    • Bowie,J.U. et al. (1996) Three-dimensional profiles for measuring compatibility of amino acid sequence with three-dimensional structure. Methods Enzymol., 266, 598-616.
    • (1996) Methods Enzymol , vol.266 , pp. 598-616
    • Bowie, J.U.1
  • 9
    • 0023984741 scopus 로고
    • The significance of protien sequence similarities
    • Collins,J.F. et al. (1988) The significance of protien sequence similarities. Comput. Appl. BioSci., 4, 67-71.
    • (1988) Comput. Appl. BioSci , vol.4 , pp. 67-71
    • Collins, J.F.1
  • 10
  • 11
    • 0030582739 scopus 로고    scopus 로고
    • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
    • Gotoh,O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J. Mol. Biol., 264, 823-838.
    • (1996) J. Mol. Biol , vol.264 , pp. 823-838
    • Gotoh, O.1
  • 12
    • 0035798406 scopus 로고    scopus 로고
    • Assignment oh homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough,J. et al. (2001) Assignment oh 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
  • 13
    • 0023375315 scopus 로고
    • Profile analysis: Detection of distantly related proteins
    • Gribskov,M. et al. (1987) Profile analysis: Detection of distantly related proteins. Proc. Natl Acad. Sci. USA, 84, 4355-4358.
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 4355-4358
    • Gribskov, M.1
  • 14
    • 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
  • 15
    • 0031721094 scopus 로고    scopus 로고
    • Homology detection via family pairwise search
    • Grundy,W.N. (1998) Homology detection via family pairwise search. J. Comput. Biol., 5, 479-491.
    • (1998) J. Comput. Biol , vol.5 , pp. 479-491
    • Grundy, W.N.1
  • 16
    • 0029887381 scopus 로고    scopus 로고
    • Hidden Markov models for sequence analysis: Extension and analysis of the basic method
    • Hughey,R. and Krogh,A. (1996) Hidden Markov models for sequence analysis: Extension and analysis of the basic method. Comput. Appl. Biosci., 12, 95-107.
    • (1996) Comput. Appl. Biosci , vol.12 , pp. 95-107
    • Hughey, R.1    Krogh, A.2
  • 17
    • 17444407069 scopus 로고    scopus 로고
    • A structure-based method for protein sequence alignment
    • Kann,M.G. et al. (2005) A structure-based method for protein sequence alignment. Bioinformatics, 21, 1451-1456.
    • (2005) Bioinformatics , vol.21 , pp. 1451-1456
    • Kann, M.G.1
  • 18
    • 0141974922 scopus 로고    scopus 로고
    • PANDORA: Keyword-based analysis of protein sets by integration of annotation sources
    • Kaplan,N. et al. (2003) PANDORA: Keyword-based analysis of protein sets by integration of annotation sources. Nucleic Acids Res., 31, 5617-5626.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5617-5626
    • Kaplan, N.1
  • 19
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin,S. and 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
  • 20
    • 0027175241 scopus 로고
    • Applications and statistics for multiple high-scoring segments in molecular sequences
    • Karlin,S. and Altschul,S.F. (1993) Applications and statistics for multiple high-scoring segments in molecular sequences. Proc. Natl Acad. Sci., 90, 5873-5877.
    • (1993) Proc. Natl Acad. Sci , vol.90 , pp. 5873-5877
    • Karlin, S.1    Altschul, S.F.2
  • 21
    • 0000586227 scopus 로고
    • Limit distributions of maximal segmental score among Markov-dependent partial sums
    • Karlin,S. and Dembo,A. (1992) Limit distributions of maximal segmental score among Markov-dependent partial sums. Adv. Appl. Prob., 24 113-140.
    • (1992) Adv. Appl. Prob , vol.24 , pp. 113-140
    • Karlin, S.1    Dembo, A.2
  • 22
    • 0032438987 scopus 로고    scopus 로고
    • (998) Hidden Markov models for detecting remote protein homologies
    • Karplus,K. et al. (998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
    • Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1
  • 23
    • 42449114481 scopus 로고    scopus 로고
    • Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT)
    • Lee,M.M. et al. (2007) Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT). Proteins, 71, 1409-1419.
    • (2007) Proteins , vol.71 , pp. 1409-1419
    • Lee, M.M.1
  • 24
    • 0002064379 scopus 로고
    • Maximum likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores
    • Mott,R. (1992) Maximum likelihood estimation of the statistical distribution of Smith-Waterman local sequence similarity scores. Bull. Math. Biol., 54, 59-75.
    • (1992) Bull. Math. Biol , vol.54 , pp. 59-75
    • Mott, R.1
  • 25
    • 0032509105 scopus 로고    scopus 로고
    • Park.J. et al. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol., 284, 1201-1210.
    • Park.J. et al. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol., 284, 1201-1210.
  • 26
    • 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
  • 27
    • 34447304880 scopus 로고    scopus 로고
    • SherLoc: High-accuracy prediction of protein subcellular localization by integrating text and protein sequence data
    • Shatkay,H. et al. (2007) SherLoc: High-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinformatics, 23, 1410-1417.
    • (2007) Bioinformatics , vol.23 , pp. 1410-1417
    • Shatkay, H.1
  • 28
  • 29
    • 0022431785 scopus 로고
    • The statistical distribution of nucleic acid similarities
    • Smith,T.F. et al. (1985) The statistical distribution of nucleic acid similarities. Nucleic Acids Res., 13, 645-656.
    • (1985) Nucleic Acids Res , vol.13 , pp. 645-656
    • Smith, T.F.1
  • 30
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson,J.D. et al. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acid Res., 27, 2682-2690.
    • (1999) Nucleic Acid Res , vol.27 , pp. 2682-2690
    • Thompson, J.D.1
  • 31
    • 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
  • 32
    • 0028234758 scopus 로고
    • Rapid and accurate estimates of statistical significance for sequence data base searches
    • Waterman,M.S. and Vingron,M. (1994) Rapid and accurate estimates of statistical significance for sequence data base searches. Proc. Natl Acad. Sci. USA, 91, 4625-4628.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 4625-4628
    • Waterman, M.S.1    Vingron, M.2


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