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Volumn , Issue SUPPL. 26, 2009, Pages

Finding similar nucleotide sequences using network blast searches

Author keywords

BLAST; Blastn; Database search; DNA; Genome; Homology search; Mapping; Megablast; Nucleic acid; RNA; Sequence alignment

Indexed keywords

RIBOSOME RNA; UNTRANSLATED RNA;

EID: 67449149966     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi0303s26     Document Type: Review
Times cited : (12)

References (41)
  • 1
    • 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
  • 5
    • 0034045656 scopus 로고    scopus 로고
    • Threedimensional model of human TIP30, a coactivator for HIV-1 Tat-activated transcription, and CC3, a protein associated with metastasis suppression
    • Baker, M.E., Yan, L., and Pear, M.R. 2000. Threedimensional model of human TIP30, a coactivator for HIV-1 Tat-activated transcription, and CC3, a protein associated with metastasis suppression. Cell Mol. Life Sci. 57:851-858.
    • (2000) Cell Mol. Life Sci. , vol.57 , pp. 851-858
    • Baker, M.E.1    Yan, L.2    Pear, M.R.3
  • 7
    • 67449153060 scopus 로고    scopus 로고
    • Assessing pairwise sequence similarity: BLAST and FASTA
    • In (A.D. Baxevanis and B.F. Ouellette, eds.), John Wiley & Sons, Hoboken, N.J
    • Baxevanis, A.D. 2005. Assessing pairwise sequence similarity: BLAST and FASTA. In Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins (A.D. Baxevanis and B.F. Ouellette, eds.), pp. 295-324. John Wiley & Sons, Hoboken, N.J.
    • (2005) Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins , pp. 295-324
    • Baxevanis, A.D.1
  • 9
    • 0030628597 scopus 로고    scopus 로고
    • Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison
    • Birney, E. and Durbin, R. 1997. Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5:56-64.
    • (1997) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.5 , pp. 56-64
    • Birney, E.1    Durbin, R.2
  • 10
  • 11
    • 0003218786 scopus 로고
    • Amodel of evolutionary change in proteins
    • In (M.O. Dayhoff, ed.), National Biomedical Research Foundation, Silver Spring, Md
    • Dayhoff, M.O. and Eck, R.V. 1968. Amodel of evolutionary change in proteins. In Atlas of Protein Sequence and Structure (M.O. Dayhoff, ed.), pp. 33-45. National Biomedical Research Foundation, Silver Spring, Md.
    • (1968) Atlas of Protein Sequence and Structure , pp. 33-45
    • Dayhoff, M.O.1    Eck, R.V.2
  • 12
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 13
    • 0036351317 scopus 로고    scopus 로고
    • Analysis of gene function in somatic mammalian cells using small interfering RNAs
    • Elbashir, S.M., Harborth, J.,Weber, K., and Tuschl, T. 2002. Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 26:199-213.
    • (2002) Methods , vol.26 , pp. 199-213
    • Elbashir, S.M.1    Harborth, J.2    Weber, K.3    Tuschl, T.4
  • 15
    • 0031762837 scopus 로고    scopus 로고
    • Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
    • Gerstein, M. 1998. Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinformatics 14:707-714.
    • (1998) Bioinformatics , vol.14 , pp. 707-714
    • Gerstein, M.1
  • 16
    • 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. U.S.A. 89:10915-10919.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 17
    • 0031829372 scopus 로고    scopus 로고
    • Removing nearneighbor redundancy from large protein sequence collections
    • Holm, L. and Sander, C. 1998. Removing nearneighbor redundancy from large protein sequence collections. Bioinformatics 14:423-429.
    • (1998) Bioinformatics , vol.14 , pp. 423-429
    • Holm, L.1    Sander, C.2
  • 20
    • 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. U.S.A. 87:2264-2268.
    • (1990) Proc. Natl. Acad. Sci. U.S.A. , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 21
    • 0027078560 scopus 로고
    • Correlation analysis of amino acid usage in protein classes
    • Karlin, S. and Bucher, P. 1992. Correlation analysis of amino acid usage in protein classes. Proc. Natl. Acad. Sci. U.S.A. 89:12165-12169.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 12165-12169
    • Karlin, S.1    Bucher, P.2
  • 23
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • Kent,W.J. 2002. BLAT - the BLAST-like alignment tool. Genome Res. 12:656-664.
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 28
    • 33745617710 scopus 로고    scopus 로고
    • A fast and symmetric DUST implementation to mask low-complexity DNA sequences
    • Morgulis, A., Gertz, E.M., Schaffer, A.A., and Agarwala, R. 2006. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J. Comput. Biol. 13:1028-1040.
    • (2006) J. Comput. Biol. , vol.13 , pp. 1028-1040
    • Morgulis, A.1    Gertz, E.M.2    Schaffer, A.A.3    Agarwala, R.4
  • 30
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: A fast search method for large DNA databases
    • Ning, Z., Cox, A.J., and Mullikin, J.C. 2001. SSAHA: A fast search method for large DNA databases. Genome Res. 11:1725-1729.
    • (2001) Genome Res. , vol.11 , pp. 1725-1729
    • Ning, Z.1    Cox, A.J.2    Mullikin, J.C.3
  • 31
    • 0032568655 scopus 로고    scopus 로고
    • SMART, a simple modular architecture research tool: Identification of signaling domains
    • Schultz, J., Milpetz, F., Bork, P., and Ponting, C.P. 1998.SMART, a simple modular architecture research tool: Identification of signaling domains. Proc. Natl. Acad. Sci. U.S.A. 95:5857-5864.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 5857-5864
    • Schultz, J.1    Milpetz, F.2    Bork, P.3    Ponting, C.P.4
  • 32
    • 40549105825 scopus 로고    scopus 로고
    • An introduction to BioPerl
    • Stajich, J.E. 2007. An introduction to BioPerl. Methods Mol. Biol. 406:535-548.
    • (2007) Methods Mol. Biol. , vol.406 , pp. 535-548
    • Stajich, J.E.1
  • 38
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wootton, J.C. and Federhen, S. 1996. Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266:554-571.
    • (1996) Methods Enzymol , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2
  • 39
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: A genomic mapping and alignment program for mRNA and EST sequences
    • Wu, T.D. and Watanabe, C.K. 2005. GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21:1859-1875.
    • (2005) Bioinformatics , vol.21 , pp. 1859-1875
    • Wu, T.D.1    Watanabe, C.K.2


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