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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. Research

    Heterochromatic sequences in a Drosophila whole-genome shotgun assembly

    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...

    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

    Genome Biology 2002 3:research0085.1

    Published on: 31 December 2002

  2. Research

    Annotation of the Drosophila melanogastereuchromatic genome: a systematic review

    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...

    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…

    Genome Biology 2002 3:research0083.1

    Published on: 31 December 2002

  3. Research

    Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophilagenome

    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...

    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…

    Genome Biology 2002 3:research0086.1

    Published on: 30 December 2002

  4. Research

    Systematic determination of patterns of gene expression during Drosophila embryogenesis

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

    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

    Genome Biology 2002 3:research0088.1

    Published on: 23 December 2002

  5. Research

    The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

    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...

    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

    Genome Biology 2002 3:research0084.1

    Published on: 23 December 2002

  6. Software

    Apollo: a sequence annotation editor

    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...

    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…

    Genome Biology 2002 3:research0082.1

    Published on: 23 December 2002

  7. Research

    A Drosophilafull-length cDNA resource

    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...

    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

    Genome Biology 2002 3:research0080.1

    Published on: 23 December 2002

  8. Research

    Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogastereuchromatic genome sequence

    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...

    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…

    Genome Biology 2002 3:research0079.1

    Published on: 23 December 2002

  9. Software

    An integrated computational pipeline and database to support whole-genome sequence annotation

    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...

    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:research0081.1

    Published on: 23 December 2002

  10. Research

    Computational analysis of core promoters in the Drosophila genome

    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...

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

    Genome Biology 2002 3:research0087.1

    Published on: 20 December 2002