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Volumn 2013, Issue 9, 2013, Pages 17-27

TIRfinder: A web tool for mining class II transposons carrying terminal inverted repeats

Author keywords

Comparative genomics; Suffix tree; Terminal inverted repeat; Transposon

Indexed keywords

AMINO ACID; DNA;

EID: 84873343262     PISSN: 11769343     EISSN: None     Source Type: Journal    
DOI: 10.4137/EBO.S10619     Document Type: Review
Times cited : (7)

References (24)
  • 1
    • 84855281420 scopus 로고    scopus 로고
    • Repetitive elements may comprise over two-thirds of the human genome
    • Dec, Epub Dec 1, 2011
    • de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. Dec 2011;7(12):e1002384. Epub Dec 1, 2011.
    • (2011) PLoS Genet , vol.7 , Issue.12
    • de Koning, A.P.1    Gu, W.2    Castoe, T.A.3    Batzer, M.A.4    Pollock, D.D.5
  • 2
    • 70450202132 scopus 로고    scopus 로고
    • The B73 maize genome: Complexity, diversity, and dynamics
    • Nov 20
    • Schnable PS, Ware D, Fulton RS, et al. The B73 maize genome: complexity, diversity, and dynamics. Science. Nov 20, 2009;326(5956):1112-5.
    • (2009) Science , vol.326 , Issue.5956 , pp. 1112-1115
    • Schnable, P.S.1    Ware, D.2    Fulton, R.S.3
  • 3
    • 42349111552 scopus 로고    scopus 로고
    • A universal classification of eukaryotic transposable elements implemented in Repbase
    • May, author reply 414
    • Kapitonov VV, Jurka J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet. May 2008;9(5):411-2; author reply 414.
    • (2008) Nat Rev Genet , vol.9 , Issue.5 , pp. 411-412
    • Kapitonov, V.V.1    Jurka, J.2
  • 4
    • 36249023071 scopus 로고    scopus 로고
    • A unified classification system for eukaryotic transposable elements
    • Dec
    • Wicker T, Sabot F, Hua-Van A, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. Dec 2007;8(12):973-82.
    • (2007) Nat Rev Genet , vol.8 , Issue.12 , pp. 973-982
    • Wicker, T.1    Sabot, F.2    Hua-Van, A.3
  • 5
    • 78650525750 scopus 로고    scopus 로고
    • Transposable element insertions have strongly affected human evolution
    • Nov 16, Epub Nov 1, 2010
    • Britten RJ. Transposable element insertions have strongly affected human evolution. Proc Natl Acad Sci U S A. Nov 16, 2010;107(46):19945-8. Epub Nov 1, 2010.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , Issue.46 , pp. 19945-19948
    • Britten, R.J.1
  • 6
    • 36549035839 scopus 로고    scopus 로고
    • Discovering and detecting transposable elementsin genome sequences
    • Nov, Epub Oct 10, 2007
    • Bergman CM, Quesneville H. Discovering and detecting transposable elementsin genome sequences. Brief Bioinform. Nov 2007;8(6):382-92. Epub Oct 10, 2007.
    • (2007) Brief Bioinform , vol.8 , Issue.6 , pp. 382-392
    • Bergman, C.M.1    Quesneville, H.2
  • 7
    • 40549086282 scopus 로고    scopus 로고
    • Computational prediction and molecular confirmation of Helitron transposons in the maize genome
    • Du C, Caronna J, He L, Dooner H. Computational prediction and molecular confirmation of Helitron transposons in the maize genome. BMC Genomics. 2008;9:51.
    • (2008) BMC Genomics , vol.9 , pp. 51
    • Du, C.1    Caronna, J.2    He, L.3    Dooner, H.4
  • 8
    • 39749179047 scopus 로고    scopus 로고
    • LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
    • Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008;9:18.
    • (2008) BMC Bioinformatics , vol.9 , pp. 18
    • Ellinghaus, D.1    Kurtz, S.2    Willhoeft, U.3
  • 9
    • 0033066718 scopus 로고    scopus 로고
    • REPuter: Fast computation of maximal repeats in complete genomes
    • May
    • Kurtz S, Schleiermacher C. REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics. May 1999;15(5):426-7.
    • (1999) Bioinformatics , vol.15 , Issue.5 , pp. 426-427
    • Kurtz, S.1    Schleiermacher, C.2
  • 10
    • 0036673472 scopus 로고    scopus 로고
    • Automated de novo identification of Repeat Sequence families in sequenced genomes
    • Bao Z, Eddy SR. Automated de novo identification of Repeat Sequence families in sequenced genomes. Genome Res. 2002;12(8):1269-76.
    • (2002) Genome Res , vol.12 , Issue.8 , pp. 1269-1276
    • Bao, Z.1    Eddy, S.R.2
  • 11
    • 6344289639 scopus 로고    scopus 로고
    • Inverted repeat structure of the human genome: The X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes
    • Oct
    • Warburton PE, Giordano J, Cheung F, Gelfand Y, Benson G. Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Res. Oct 2004;14(10A):1861-9.
    • (2004) Genome Res , vol.14 , Issue.10 A , pp. 1861-1869
    • Warburton, P.E.1    Giordano, J.2    Cheung, F.3    Gelfand, Y.4    Benson, G.5
  • 12
    • 0043123038 scopus 로고    scopus 로고
    • MAK, a computational tool kit for automated MITE analysis
    • Jul 1
    • Yang G, Hall TC. MAK, a computational tool kit for automated MITE analysis. Nucleic Acids Res. Jul 1, 2003;31(13):3659-65.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3659-3665
    • Yang, G.1    Hall, T.C.2
  • 13
    • 78650432054 scopus 로고    scopus 로고
    • MITE-Hunter: A program for discovering miniature inverted-repeat transposable elements from genomic sequences
    • Dec, Epub Sep 29, 2010
    • Han Y, Wessler SR. MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res. Dec 2010;38(22):e199. Epub Sep 29, 2010.
    • (2010) Nucleic Acids Res , vol.38 , Issue.22
    • Han, Y.1    Wessler, S.R.2
  • 14
    • 62549105255 scopus 로고    scopus 로고
    • MUST: A system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi
    • May 1, Epub Feb 10, 2009
    • Chen Y, Zhou F, Li G, Xu Y. MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi. Gene. May 1, 2009;436(1-2):1-7. Epub Feb 10, 2009.
    • (2009) Gene , vol.436 , Issue.1-2 , pp. 1-7
    • Chen, Y.1    Zhou, F.2    Li, G.3    Xu, Y.4
  • 15
    • 28944444049 scopus 로고    scopus 로고
    • Suffix-tree analyser (STAN): Looking for nucleotidic and peptidic patterns in chromosomes
    • Dec 15, Epub Oct 13, 2005
    • Nicolas J, Durand P, Ranchy G, Tempel S, Valin AS. Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes. Bioinformatics. Dec 15, 2005;21(24):4408-10. Epub Oct 13, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4408-4410
    • Nicolas, J.1    Durand, P.2    Ranchy, G.3    Tempel, S.4    Valin, A.S.5
  • 16
    • 0036900064 scopus 로고    scopus 로고
    • Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana
    • Dec
    • Santiago N, Herráiz C, Goñi JR, Messeguer X, Casacuberta JM. Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana. Mol Biol Evol. Dec 2002;19(12):2285-93.
    • (2002) Mol Biol Evol , vol.19 , Issue.12 , pp. 2285-2293
    • Santiago, N.1    Herráiz, C.2    Goñi, J.R.3    Messeguer, X.4    Casacuberta, J.M.5
  • 17
    • 0022422660 scopus 로고
    • Nomenclature for incompletely specified bases in nucleic acid sequences: Recommendations 1984
    • May 10
    • Cornish-Bowden A. Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. May 10, 1985;13(9):3021-30.
    • (1985) Nucleic Acids Res , vol.13 , Issue.9 , pp. 3021-3030
    • Cornish-Bowden, A.1
  • 18
    • 38649116613 scopus 로고    scopus 로고
    • Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula
    • Nov 9
    • Grzebelus D, Lasota S, Gambin T, Kucherov G, Gambin A. Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula. BMC Genomics. Nov 9, 2007;8:409.
    • (2007) BMC Genomics , vol.8 , pp. 409
    • Grzebelus, D.1    Lasota, S.2    Gambin, T.3    Kucherov, G.4    Gambin, A.5
  • 19
    • 70350231372 scopus 로고    scopus 로고
    • Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago
    • Dec 15, Epub Jun 17, 2009
    • Grzebelus D, Gładysz M, Macko-Podgórni A, et al. Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago Gene. Dec 15, 2009;448(2):214-20. Epub Jun 17, 2009.
    • (2009) Gene , vol.448 , Issue.2 , pp. 214-220
    • Grzebelus, D.1    Gładysz, M.2    Macko-Podgórni, A.3
  • 20
    • 77954854627 scopus 로고    scopus 로고
    • Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
    • Jul 15
    • Novák P, Neumann P, Macas J. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics. Jul 15, 2010;11:378.
    • (2010) BMC Bioinformatics , vol.11 , pp. 378
    • Novák, P.1    Neumann, P.2    Macas, J.3
  • 22
    • 1042307072 scopus 로고    scopus 로고
    • Transposon diversity in Arabidopsis thaliana
    • Jun 20
    • Le QH, Wright S, Yu Z, Bureau T. Transposon diversity in Arabidopsis thaliana. Proc Natl Acad Sci U S A. Jun 20, 2000;97(13):7376-81.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , Issue.13 , pp. 7376-7381
    • Le, Q.H.1    Wright, S.2    Yu, Z.3    Bureau, T.4
  • 24
    • 56049109767 scopus 로고    scopus 로고
    • Different strategies to persist: The pogo-like Lemi1 transposon produces miniature inverted-repeat transposable elements or typical defective elements in different plant genomes
    • Sep, Epub Aug 30, 2008
    • Guermonprez H, Loot C, Casacuberta JM. Different strategies to persist: the pogo-like Lemi1 transposon produces miniature inverted-repeat transposable elements or typical defective elements in different plant genomes. Genetics. Sep 2008;180(1):83-92. Epub Aug 30, 2008.
    • (2008) Genetics , vol.180 , Issue.1 , pp. 83-92
    • Guermonprez, H.1    Loot, C.2    Casacuberta, J.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.