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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:research0081-0081.11 doi:10.1186/gb-2002-3-12-research0081

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Computational identification of Drosophila microRNA genes

Eric C Lai, Pavel Tomancak, Robert W Williams, Gerald M Rubin Genome Biology 2003, 4:R42 (30 June 2003)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

An informatic procedure has been used to analyze the euchromatic sequences of Drosophila melanogaster and D. pseudoobscura for conserved sequences that adopt an extended stem-loop structure and display other characteristics of known miRNAs.

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Impressive expressions: developing a systematic database of gene-expression patterns in Drosophila embryogenesis

Haiqiong Montalta-He, Heinrich Reichert Genome Biology 2003, 4:205 (28 January 2003)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

The establishment of a database of gene-expression patterns derived from systematic highthroughput in situ hybridization studies on whole-mount Drosophila embryos vastly increases the breadth and depth that can be reached by developmental genetics.

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Heterochromatic sequences in a Drosophila whole-genome shotgun assembly

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, Gary H Karpen Genome Biology 2002, 3:research0085-0085.16 (31 December 2002)

This article is part of a collection on Release 3 of the...

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

Annotation of an improved whole-genome shotgun assembly of the Drosophila melanogaster genome predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Fluorescence in situ hybridization was used to correlate the genomic sequence with the cytogenetic map; the annotated euchromatic sequence extends into the centric heterochromatin on each chromosome arm.

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Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

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, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, ShengQiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis Genome Biology 2002, 3:research0083-0083.22 (31 December 2002)

This article is part of a collection on Release 3 of the...

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.

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Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-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, Susan E Celniker Genome Biology 2002, 3:research0086-0086.20 (30 December 2002)

This article is part of a collection on Release 3 of the...

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Analysis of conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons.

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Systematic determination of patterns of gene expression during Drosophila embryogenesis

Pavel Tomancak, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2002, 3:research0088-0088.14 (23 December 2002)

This article is part of a collection on Release 3 of the...

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, 2,179 genes have been examinded by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos.

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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, ME Clamp Genome Biology 2002, 3:research0082-0082.14 (23 December 2002)

This article is part of a collection on Release 3 of the...

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | F1000 Biology | Editor’s summary

Apollo was developed to enable curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome.

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

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, Joanne M Pacleb, Soo Park, Barret D Pfeiffer, Stephen Richards, Erica J Sodergren, Robert Svirskas, Paul E Tabor, Kenneth Wan, Mark Stapleton, Granger G Sutton, Craig Venter, George Weinstock, Steven E Scherer, Eugene W Myers, Richard A Gibbs, Gerald M Rubin et al. Genome Biology 2002, 3:research0079-0079.14 (23 December 2002)

This article is part of a collection on Release 3 of the...

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

The Drosophila melanogaster genome was the first metazoan genome to be sequenced by whole-genome shotgun. Now, the sequence has been finished in a process designed to close gaps, improve sequence quality and validate the assembly.

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