Release 3 of the Drosophila genome

A series of refereed research articles from Berkeley Drosophila Genome Project, FlyBase and colleagues, describing Release 3 of the Drosophila genome, are freely available online. The articles describe the finishing and annotation of the genome sequence, computational tools, and functional studies.

research Finishing a whole genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence SE Celniker, DA Wheeler, B Kronmiller, JW Carlson, A Halpern, S Patel, M Adams, M Champe, SP Dugan, E Frise, A Hodgson , RA George, RA Hoskins, T Laverty, DM Muzny, CR Nelson, JM Pacleb, S Park, BD Pfeiffer, S Richards, EJ Sodergren, R Svirskas, PE Tabor, K Wan, M Stapleton, GG Sutton, C Venter, G Weinstock, SE Scherer, EW Myers, RA Gibbs and GM Rubin Genome Biology 2002, 3(12):research0079 [Abstract] [Full text] [PDF]

research A Drosophila full-length cDNA resource M Stapleton, J Carlson, P Brokstein, C Yu, M Champe, R George, H Guarin, B Kronmiller, J Pacleb, S Park, K Wan, GM Rubin and SE Celniker Genome Biology 2002, 3(12):research0080 [Abstract] [Full text] [PDF]

software An integrated computational pipeline and database to support whole-genome sequence annotation CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin and SE Lewis Genome Biology 2002, 3(12):research0081 [Abstract] [Full text] [PDF]

software Apollo: a sequence annotation editor SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall and ME Clamp Genome Biology 2002, 3(12):research0082 [Abstract] [Full text] [PDF]

research Annotation of the Drosophila melanogaster euchromatic genome: a systematic review S Misra, MA Crosby, CJ Mungall, BB Matthews, KS Campbell, P Hradecky, Y Huang, JS Kaminker, GH Millburn, SE Prochnik, CD Smith, JL Tupy, EJ Whitfield, L Bayraktaroglu, BP Berman, BR Bettencourt, SE Celniker, ADNJ de Grey, RA Drysdale, NL Harris, J Richter, S Russo, AJ Schroeder, SQ Shu, M Stapleton, C Yamada, M Ashburner, WM Gelbart, GM Rubin and SE Lewis Genome Biology 2002, 3(12):research0083 [Abstract] [Full text] [PDF]

research The transposable elements of the Drosophila melanogaster euchromatin - a genomics perspective JS Kaminker, CM Bergman, B Kronmiller, J Carlson, R Svirskas, S Patel, E Frise, DA Wheeler, SE Lewis, GM Rubin, M Ashburner and SE Celniker Genome Biology 2002, 3(12):research0084 [Abstract] [Full text] [PDF]

research Heterochromatic sequences in a Drosophila whole genome shotgun assembly RA Hoskins, CD Smith, JW Carlson, AB Carvalho, A Halpern, JS Kaminker, C Kennedy, CJ Mungall, BA Sullivan, GG Sutton, JC Yasuhara, BT Wakimoto, EW Myers, SE Celniker, GM Rubin and GH Karpen Genome Biology 2002, 3(12):research0085 [Abstract] [Full text] [PDF]

research Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome CM Bergman, BD Pfeiffer, DE Rincón-Limas, RA Hoskins, A Gnirke, CJ Mungall, AM Wang, B Kronmiller, J Pacleb, S Park, M Stapleton, K Wan, RA George, PJ de Jong, J Botas, GM Rubin and SE Celniker Genome Biology 2002, 3(12):research0086 [Abstract] [Full text] [PDF]

research Computational analysis of core promoters in the Drosophila genome U Ohler, G-c Liao, H Niemann and GM Rubin Genome Biology 2002, 3(12):research0087 [Abstract] [Full text] [PDF]

research Systematic determination of patterns of gene expression during Drosophila embryogenesis P Tomancak, A Beaton, R Weiszmann, E Kwan, S Shu, SE Lewis, S Richards, M Ashburner, V Hartenstein, SE Celniker and GM Rubin Genome Biology 2002, 3(12):research0088 [Abstract] [Full text] [PDF]

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