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    Results: 1 to 20 of 103

    1.

    Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.

    Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR.

    Genome Biol. 2008 Jan 11;9(1):R7.

    PMID:
    18190707
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome.

    Thibaud-Nissen F, Campbell M, Hamilton JP, Zhu W, Buell CR.

    BMC Genomics. 2007 Oct 25;8:388.

    PMID:
    17961238
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.

    Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O.

    Nucleic Acids Res. 2003 Oct 1;31(19):5654-66.

    PMID:
    14500829
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    The institute for genomic research Osa1 rice genome annotation database.

    Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR.

    Plant Physiol. 2005 May;138(1):18-26.

    PMID:
    15888674
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    EAnnot: a genome annotation tool using experimental evidence.

    Ding L, Sabo A, Berkowicz N, Meyer RR, Shotland Y, Johnson MR, Pepin KH, Wilson RK, Spieth J.

    Genome Res. 2004 Dec;14(12):2503-9.

    PMID:
    15574829
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

    Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE.

    Genome Biol. 2002;3(12):RESEARCH0083. Epub 2002 Dec 31. Review.

    PMID:
    12537572
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    GeneSeqer@PlantGDB: Gene structure prediction in plant genomes.

    Schlueter SD, Dong Q, Brendel V.

    Nucleic Acids Res. 2003 Jul 1;31(13):3597-600.

    PMID:
    12824374
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    The GAIA software framework for genome annotation.

    Overton GC, Bailey C, Crabtree J, Gibson M, Fischer S, Schug J.

    Pac Symp Biocomput. 1998:291-302.

    PMID:
    9697190
    [PubMed - indexed for MEDLINE]
    Free Article
    10.

    Gene and alternative splicing annotation with AIR.

    Florea L, Di Francesco V, Miller J, Turner R, Yao A, Harris M, Walenz B, Mobarry C, Merkulov GV, Charlab R, Dew I, Deng Z, Istrail S, Li P, Sutton G.

    Genome Res. 2005 Jan;15(1):54-66.

    PMID:
    15632090
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists.

    Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR.

    Nucleic Acids Res. 2003 Jan 1;31(1):229-33.

    PMID:
    12519988
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    12.

    RiceGAAS: an automated annotation system and database for rice genome sequence.

    Sakata K, Nagamura Y, Numa H, Antonio BA, Nagasaki H, Idonuma A, Watanabe W, Shimizu Y, Horiuchi I, Matsumoto T, Sasaki T, Higo K.

    Nucleic Acids Res. 2002 Jan 1;30(1):98-102.

    PMID:
    11752265
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

    Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.

    PLoS Biol. 2004 Jun;2(6):e162. Epub 2004 Apr 20. Erratum in: PLoS Biol. 2004 Jul;2(7):e256.

    PMID:
    15103394
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features.

    Schlueter SD, Wilkerson MD, Dong Q, Brendel V.

    Genome Biol. 2006;7(11):R111.

    PMID:
    17116260
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    JIGSAW: integration of multiple sources of evidence for gene prediction.

    Allen JE, Salzberg SL.

    Bioinformatics. 2005 Sep 15;21(18):3596-603. Epub 2005 Aug 2.

    PMID:
    16076884
    [PubMed - indexed for MEDLINE]
    Free Article
    16.

    Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES.

    Borodovsky M, Lomsadze A.

    Curr Protoc Bioinformatics. 2011 Sep;Chapter 4:Unit 4.6.1-10.

    PMID:
    21901742
    [PubMed - indexed for MEDLINE]
    17.

    Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae.

    Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA.

    BMC Microbiol. 2009 Feb 19;9 Suppl 1:S8. Review.

    PMID:
    19278556
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    Development and evaluation of an automated annotation pipeline and cDNA annotation system.

    Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J.

    Genome Res. 2003 Jun;13(6B):1542-51.

    PMID:
    12819153
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    19.

    Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome.

    D'Agostino N, Traini A, Frusciante L, Chiusano ML.

    BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S9.

    PMID:
    17430576
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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