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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.

  1. Content type: Research

    Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it dif...

    Authors: Roger A Hoskins, Christopher D Smith, Joseph W Carlson, A Bernardo Carvalho, Aaron Halpern, Joshua S Kaminker, Cameron Kennedy, Chris J Mungall, Beth A Sullivan, Granger G Sutton, Jiro C Yasuhara, Barbara T Wakimoto, Eugene W Myers, Susan E Celniker, Gerald M Rubin and Gary H Karpen

    Citation: Genome Biology 2002 3:research0085.1

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  2. Content type: Research

    The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic gene...

    Authors: Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfield, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt…

    Citation: Genome Biology 2002 3:research0083.1

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  3. Content type: Research

    It is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be de...

    Authors: Casey M Bergman, Barret D Pfeiffer, Diego E Rinc√≥n-Limas, Roger A Hoskins, Andreas Gnirke, Chris J Mungall, Adrienne M Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A George, Pieter J de Jong, Juan Botas, Gerald M Rubin…

    Citation: Genome Biology 2002 3:research0086.1

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  4. Content type: Research

    Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription.

    Authors: Pavel Tomancak, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker and Gerald M Rubin

    Citation: Genome Biology 2002 3:research0088.1

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  5. Content type: Research

    Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project ha...

    Authors: Joshua S Kaminker, Casey M Bergman, Brent Kronmiller, Joseph Carlson, Robert Svirskas, Sandeep Patel, Erwin Frise, David A Wheeler, Suzanna E Lewis, Gerald M Rubin, Michael Ashburner and Susan E Celniker

    Citation: Genome Biology 2002 3:research0084.1

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  6. Content type: Software

    The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and indepe...

    Authors: 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…

    Citation: Genome Biology 2002 3:research0082.1

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  7. Content type: Research

    A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes. Providing this resource to the Drosophila...

    Authors: Mark Stapleton, Joe Carlson, Peter Brokstein, Charles Yu, Mark Champe, Reed George, Hannibal Guarin, Brent Kronmiller, Joanne Pacleb, Soo Park, Ken Wan, Gerald M Rubin and Susan E Celniker

    Citation: Genome Biology 2002 3:research0080.1

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  8. Content type: Research

    The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were widely debated in the genomics commun...

    Authors: Susan E Celniker, David A Wheeler, Brent Kronmiller, Joseph W Carlson, Aaron Halpern, Sandeep Patel, Mark Adams, Mark Champe, Shannon P Dugan, Erwin Frise, Ann Hodgson, Reed A George, Roger A Hoskins, Todd Laverty, Donna M Muzny, Catherine R Nelson…

    Citation: Genome Biology 2002 3:research0079.1

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  9. Content type: Software

    We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale g...

    Authors: 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

    Citation: Genome Biology 2002 3:research0081.1

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  10. Content type: Research

    The core promoter, a region of about 100 base-pairs flanking the transcription start site (TSS), serves as the recognition site for the basal transcription apparatus. Drosophila TSSs have generally been mapped by...

    Authors: Uwe Ohler, Guo-chun Liao, Heinrich Niemann and Gerald M Rubin

    Citation: Genome Biology 2002 3:research0087.1

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