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    Results: 1 to 20 of 195

    1.

    A clustering method for repeat analysis in DNA sequences.

    Volfovsky N, Haas BJ, Salzberg SL.

    Genome Biol. 2001;2(8):RESEARCH0027. Epub 2001 Aug 1.

    PMID:
    11532211
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

    Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H.

    Science. 2002 Apr 5;296(5565):79-92.

    PMID:
    11935017
    [PubMed - indexed for MEDLINE]
    3.

    Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals.

    Reneker J, Shyu CR.

    BMC Bioinformatics. 2005 May 3;6:111.

    PMID:
    15869708
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.

    Kurtz S, Narechania A, Stein JC, Ware D.

    BMC Genomics. 2008 Oct 31;9:517.

    PMID:
    18976482
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    A BAC end view of the Musa acuminata genome.

    Cheung F, Town CD.

    BMC Plant Biol. 2007 Jun 11;7:29.

    PMID:
    17562019
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences.

    Hane JK, Oliver RP.

    BMC Bioinformatics. 2008 Nov 12;9:478.

    PMID:
    19014496
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties.

    Masoudi-Nejad A, Movahedi S, Jáuregui R.

    BMC Genomics. 2011 May 6;12:214. doi: 10.1186/1471-2164-12-214.

    PMID:
    21548945
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project.

    Salse J, Piégu B, Cooke R, Delseny M.

    Nucleic Acids Res. 2002 Jun 1;30(11):2316-28.

    PMID:
    12034818
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).

    Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S.

    Science. 2002 Apr 5;296(5565):92-100.

    PMID:
    11935018
    [PubMed - indexed for MEDLINE]
    10.

    GATA: a graphic alignment tool for comparative sequence analysis.

    Nix DA, Eisen MB.

    BMC Bioinformatics. 2005 Jan 17;6:9.

    PMID:
    15655071
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome.

    Becher V, Deymonnaz A, Heiber P.

    Bioinformatics. 2009 Jul 15;25(14):1746-53. Epub 2009 May 18.

    PMID:
    19451169
    [PubMed - indexed for MEDLINE]
    Free Article
    12.

    The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice.

    Vandepoele K, Saeys Y, Simillion C, Raes J, Van De Peer Y.

    Genome Res. 2002 Nov;12(11):1792-801.

    PMID:
    12421767
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

    Yavatkar AS, Lin Y, Ross J, Fann Y, Brody T, Odenwald WF.

    BMC Genomics. 2008 Feb 28;9:106.

    PMID:
    18307801
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    FORRepeats: detects repeats on entire chromosomes and between genomes.

    Lefebvre A, Lecroq T, Dauchel H, Alexandre J.

    Bioinformatics. 2003 Feb 12;19(3):319-26.

    PMID:
    12584116
    [PubMed - indexed for MEDLINE]
    Free Article
    15.

    Genome cluster database. A sequence family analysis platform for Arabidopsis and rice.

    Horan K, Lauricha J, Bailey-Serres J, Raikhel N, Girke T.

    Plant Physiol. 2005 May;138(1):47-54.

    PMID:
    15888677
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    16.

    JunctionViewer: customizable annotation software for repeat-rich genomic regions.

    Wolfgruber TK, Presting GG.

    BMC Bioinformatics. 2010 Jan 12;11:23.

    PMID:
    20067643
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    17.

    Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey.

    Swaminathan K, Varala K, Hudson ME.

    BMC Genomics. 2007 May 24;8:132.

    PMID:
    17524145
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    PILER: identification and classification of genomic repeats.

    Edgar RC, Myers EW.

    Bioinformatics. 2005 Jun;21 Suppl 1:i152-8.

    PMID:
    15961452
    [PubMed - indexed for MEDLINE]
    Free Article
    19.

    De novo repeat classification and fragment assembly.

    Pevzner PA, Tang H, Tesler G.

    Genome Res. 2004 Sep;14(9):1786-96. Erratum in: Genome Res. 2004 Dec;14(12):2510. Pevzner, Paul A [corrected to Pevzner, Pavel A].

    PMID:
    15342561
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    20.

    454 sequencing put to the test using the complex genome of barley.

    Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N.

    BMC Genomics. 2006 Oct 26;7:275.

    PMID:
    17067373
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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