메뉴 건너뛰기




Volumn 38, Issue 7, 2010, Pages 2177-2189

Homologous over-extension: A challenge for iterative similarity searches

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; CONTROLLED STUDY; DNA LIBRARY; EXTENSION GENE; FALSE POSITIVE RESULT; GENE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; CHEMISTRY; CLASSIFICATION; GENETICS; METHODOLOGY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

EID: 77952296596     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1219     Document Type: Article
Times cited : (51)

References (28)
  • 2
    • 0033990061 scopus 로고    scopus 로고
    • Flexible sequence similarity searching with the FASTA3 program package
    • Pearson,W.R. (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol., 132, 185-219.
    • (2000) Methods Mol. Biol. , vol.132 , pp. 185-219
    • Pearson, W.R.1
  • 3
    • 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
  • 4
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 5
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner,S.E., Chothia,C. and Hubbard,T.J. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA, 95, 6073-6078.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 6073-6078
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 6
    • 0029006770 scopus 로고
    • Comparison of methods for searching protein sequence databases
    • Pearson,W.R. (1995) Comparison of methods for searching protein sequence databases. Protein Sci., 4, 1145-1160.
    • (1995) Protein Sci. , vol.4 , pp. 1145-1160
    • Pearson, W.R.1
  • 7
    • 20444449200 scopus 로고    scopus 로고
    • The limits of protein sequence comparison?
    • Pearson,W.R. and Sierk,M.L. (2005) The limits of protein sequence comparison? Curr. Opin. Struct. Biol., 15, 254-260.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 254-260
    • Pearson, W.R.1    Sierk, M.L.2
  • 9
    • 1342289274 scopus 로고    scopus 로고
    • Sensitivity and selectivity in protein structure comparison
    • Sierk,M.L. and Pearson,W.R. (2004) Sensitivity and selectivity in protein structure comparison. Protein Sci., 13, 773-785.
    • (2004) Protein Sci. , vol.13 , pp. 773-785
    • Sierk, M.L.1    Pearson, W.R.2
  • 10
    • 67849085006 scopus 로고    scopus 로고
    • SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches
    • Lee,M.M., Chan,M.K. and Bundschuh,R. (2009) SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches. Nucleic Acids Res., 37, W53-W56.
    • (2009) Nucleic Acids Res. , vol.37
    • Lee, M.M.1    Chan, M.K.2    Bundschuh, R.3
  • 12
    • 46249130240 scopus 로고    scopus 로고
    • The effectiveness of position-and composition-specific gap costs for protein similarity searches
    • Stojmirovic,A., Gertz,E.M., Altschul,S.F. and Yu,Y.K. (2008) The effectiveness of position-and composition-specific gap costs for protein similarity searches. Bioinformatics, 24, i15-i23.
    • (2008) Bioinformatics , vol.24
    • Stojmirovic, A.1    Gertz, E.M.2    Altschul, S.F.3    Yu, Y.K.4
  • 13
    • 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., Chan,M.K. and Bundschuh,R. (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    Chan, M.K.2    Bundschuh, R.3
  • 16
    • 0030861438 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence data bank and its supplement TrEMBL
    • Bairoch,A. and Apweiler,R. (1997) The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucleic Acids Res., 25, 31-36.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 31-36
    • Bairoch, A.1    Apweiler, R.2
  • 17
    • 75849153303 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) in 2010
    • UniProt Consortium
    • UniProt Consortium. (2009) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
    • (2009) Nucleic Acids Res. , vol.38
  • 18
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 20
    • 0036857358 scopus 로고    scopus 로고
    • QuickTree: building huge neighbour-joining trees of protein sequences
    • Howe,K., Bateman,A. and Durbin,R. (2002) QuickTree: building huge neighbour-joining trees of protein sequences. Bioinformatics, 18, 1546-1547.
    • (2002) Bioinformatics , vol.18 , pp. 1546-1547
    • Howe, K.1    Bateman, A.2    Durbin, R.3
  • 22
    • 0033492834 scopus 로고    scopus 로고
    • Post-processing long pairwise alignments
    • Zhang,Z., Berman,P., Wiehe,T. and Miller,W. (1999) Post-processing long pairwise alignments. Bioinformatics, 15, 1012-1019.
    • (1999) Bioinformatics , vol.15 , pp. 1012-1019
    • Zhang, Z.1    Berman, P.2    Wiehe, T.3    Miller, W.4
  • 23
    • 0035863762 scopus 로고    scopus 로고
    • The estimation of statistical parameters for local alignment score distributions
    • Altschul,S.F., Bundschuh,R., Olsen,R. and Hwa,T. (2001) The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Res., 29, 351-361.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 351-361
    • Altschul, S.F.1    Bundschuh, R.2    Olsen, R.3    Hwa, T.4
  • 27
    • 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
  • 28
    • 0042594474 scopus 로고    scopus 로고
    • SATCHMO: sequence alignment and tree construction using hidden Markov models
    • Edgar,R.C. and Sjolander,K. (2003) SATCHMO: sequence alignment and tree construction using hidden Markov models. Bioinformatics, 19, 1404-1411.
    • (2003) Bioinformatics , vol.19 , pp. 1404-1411
    • Edgar, R.C.1    Sjolander, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.