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Volumn 44, Issue D1, 2016, Pages D81-D89

The Dfam database of repetitive DNA families

Author keywords

[No Author keywords available]

Indexed keywords

REPETITIVE DNA; DNA; TRANSPOSON;

EID: 84976871290     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1272     Document Type: Article
Times cited : (476)

References (30)
  • 1
    • 0036673472 scopus 로고    scopus 로고
    • Automated de novo identification of repeat sequence families in sequenced genomes
    • Bao, Z. and Eddy, S.R. (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res., 12, 1269-1276.
    • (2002) Genome Res. , vol.12 , pp. 1269-1276
    • Bao, Z.1    Eddy, S.R.2
  • 3
    • 79551624472 scopus 로고    scopus 로고
    • Considering transposable element diversification in de novo annotation approaches
    • Flutre, T., Duprat, E., Feuillet, C. and Quesneville, H. (2011) Considering transposable element diversification in de novo annotation approaches. PLoS ONE, 6, e16526.
    • (2011) PLoS ONE , vol.6
    • Flutre, T.1    Duprat, E.2    Feuillet, C.3    Quesneville, H.4
  • 4
    • 33750831582 scopus 로고    scopus 로고
    • Annotation, submission and screening of repetitive elements in repbase: Repbasesubmitter and censor
    • Kohany, O., Gentles, A., Hankus, L. and Jurka, J. (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics, 7, 474.
    • (2006) BMC Bioinformatics , vol.7 , pp. 474
    • Kohany, O.1    Gentles, A.2    Hankus, L.3    Jurka, J.4
  • 5
    • 77956964275 scopus 로고    scopus 로고
    • An introduction to hidden Markov models for biological sequences. In: Searls, D and kasif, S (eds)
    • Elsevier
    • Krogh, A. (1998) An Introduction to Hidden Markov Models for Biological Sequences. In: Searls, D and Kasif, S (eds). Computational Methods in Molecular Biology. Elsevier, pp. 45-63.
    • (1998) Computational Methods in Molecular Biology , pp. 45-63
    • Krogh, A.1
  • 10
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy, S.R. (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform., 23, 205-211.
    • (2009) Genome Inform. , vol.23 , pp. 205-211
    • Eddy, S.R.1
  • 11
    • 84892432106 scopus 로고    scopus 로고
    • Nhmmer: DNA homology search with profile HMMs
    • Wheeler, T.J. and Eddy, S.R. (2013) nhmmer: DNA homology search with profile HMMs. Bioinformatics, 29, 2487-2489.
    • (2013) Bioinformatics , vol.29 , pp. 2487-2489
    • Wheeler, T.J.1    Eddy, S.R.2
  • 12
    • 84930641238 scopus 로고    scopus 로고
    • Repbase update, a database of repetitive elements in Eukaryotic genomes
    • Bao, W., Kojima, K.K. and Kohany, O. (2015) Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob. DNA, 6, 11.
    • (2015) Mob. DNA , vol.6 , pp. 11
    • Bao, W.1    Kojima, K.K.2    Kohany, O.3
  • 13
    • 84946023382 scopus 로고    scopus 로고
    • Type material in the NCBI taxonomy database
    • Federhen, S. (2015) Type material in the NCBI Taxonomy Database. Nucleic Acids Res., 43, D1086-D1098.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D1086-D1098
    • Federhen, S.1
  • 15
    • 84877940570 scopus 로고    scopus 로고
    • HAL: A hierarchical format for storing and analyzing multiple genome alignments
    • Hickey, G., Paten, B., Earl, D., Zerbino, D. and Haussler, D. (2013) HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics, 29, 1341-1342.
    • (2013) Bioinformatics , vol.29 , pp. 1341-1342
    • Hickey, G.1    Paten, B.2    Earl, D.3    Zerbino, D.4    Haussler, D.5
  • 16
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 573-580
    • Benson, G.1
  • 18
    • 77952296596 scopus 로고    scopus 로고
    • Homologous over-extension: A challenge for iterative similarity searches
    • Gonzalez, M.W. and Pearson, W.R. (2010) Homologous over-extension: a challenge for iterative similarity searches. Nucleic Acids Res., 38, 2177-2189.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2177-2189
    • Gonzalez, M.W.1    Pearson, W.R.2
  • 19
    • 84903960896 scopus 로고    scopus 로고
    • Realistic artificial DNA sequences as negative controls for computational genomics
    • Caballero, J., Smit, A.F.A., Hood, L. and Glusman, G. (2014) Realistic artificial DNA sequences as negative controls for computational genomics. Nucleic Acids Res., 42, e99.
    • (2014) Nucleic Acids Res. , vol.42 , pp. e99
    • Caballero, J.1    Smit, A.F.A.2    Hood, L.3    Glusman, G.4
  • 20
    • 0343804994 scopus 로고
    • Sequence organization and genomic distribution of the major family of interspersed repeats of mouse DNA
    • Meunier-Rotival, M., Soriano, P., Cuny, G., Strauss, F. and Bernardi, G. (1982) Sequence organization and genomic distribution of the major family of interspersed repeats of mouse DNA. Proc. Natl. Acad. Sci. U. S. A., 79, 355-359.
    • (1982) Proc. Natl. Acad. Sci. U. S. A. , vol.79 , pp. 355-359
    • Meunier-Rotival, M.1    Soriano, P.2    Cuny, G.3    Strauss, F.4    Bernardi, G.5
  • 21
    • 0010314873 scopus 로고
    • The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes
    • Soriano, P., Meunier-Rotival, M. and Bernardi, G. (1983) The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes. Proc. Natl. Acad. Sci. U.S.A, 80, 1816-1820.
    • (1983) Proc. Natl. Acad. Sci. U.S.A , vol.80 , pp. 1816-1820
    • Soriano, P.1    Meunier-Rotival, M.2    Bernardi, G.3
  • 22
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul, S. (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.1
  • 24
    • 54549109145 scopus 로고    scopus 로고
    • The whole alignment and nothing but the alignment: The problem of spurious alignment fanks
    • Frith, M.C., Park, Y., Sheetlin, S.L. and Spouge, J.L. (2008) The whole alignment and nothing but the alignment: the problem of spurious alignment fanks. Nucleic Acids Res., 36, 5863-5871.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5863-5871
    • Frith, M.C.1    Park, Y.2    Sheetlin, S.L.3    Spouge, J.L.4
  • 25
    • 84890079059 scopus 로고    scopus 로고
    • Adjusting scoring matrices to correct overextended alignments
    • Mills, L.J. and Pearson, W.R. (2013) Adjusting scoring matrices to correct overextended alignments. Bioinformatics, 29, 3007-3013.
    • (2013) Bioinformatics , vol.29 , pp. 3007-3013
    • Mills, L.J.1    Pearson, W.R.2
  • 26
    • 0029098961 scopus 로고
    • Meiotic recombination, noncoding DNA and genomic organization in caenorhabditis elegans
    • Barnes, T.M., Kohara, Y., Coulson, A. and Hekimi, S. (1995) Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics, 141, 159-179.
    • (1995) Genetics , vol.141 , pp. 159-179
    • Barnes, T.M.1    Kohara, Y.2    Coulson, A.3    Hekimi, S.4
  • 27
    • 0034602786 scopus 로고    scopus 로고
    • Repetitive-DNA elements are similarly distributed on caenorhabditis elegans autosomes
    • Surzycki, S.A. and Belknap, W.R. (2000) Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes. Proc. Natl. Acad. Sci. U.S.A., 97, 245-249.
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 245-249
    • Surzycki, S.A.1    Belknap, W.R.2
  • 28
    • 0028804572 scopus 로고
    • MIRs are classic, tRNA-derived SINEs that amplified before the Mammalian radiation
    • Smit, A.F.A. and Riggs, A.D. (1995) MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation. Nucleic Acids Res., 23, 98-102.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 98-102
    • Smit, A.F.A.1    Riggs, A.D.2
  • 29
    • 0033017956 scopus 로고    scopus 로고
    • CORE-SINEs: Eukaryotic short interspersed retroposing elements with common sequence motifs
    • Gilbert, N. and Labuda, D. (1999) CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs. Proc. Natl. Acad. Sci. U.S.A., 96, 2869-2874.
    • (1999) Proc. Natl. Acad. Sci. U.S.A. , vol.96 , pp. 2869-2874
    • Gilbert, N.1    Labuda, D.2
  • 30
    • 84901004210 scopus 로고    scopus 로고
    • Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression
    • Jjingo, D., Conley, A.B., Wang, J., Mariño-Ramírez, L., Lunyak, V.V. and Jordan, I.K. (2014) Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. Mob. DNA, 5, 14.
    • (2014) Mob. DNA , vol.5 , pp. 14
    • Jjingo, D.1    Conley, A.B.2    Wang, J.3    Mariño-Ramírez, L.4    Lunyak, V.V.5    Jordan, I.K.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.