Apollo: a sequence annotation editor
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* Corresponding author: SE Lewis suzi@fruitfly.org
Genome Biology 2002, 3:research0082-0082.14 doi:10.1186/gb-2002-3-12-research0082
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BioMed Central: 32 citations
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Research article
Kounthéa Phok, Annick Moisan, Dana Rinaldi, Nicolas Brucato, Agamemnon J Carpousis, Christine Gaspin, Béatrice Clouet-d'Orval BMC Genomics 2011, 12:312 (13 June 2011) |
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Method
A standard variation file format for human genome sequences Martin G Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor T Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck Genome Biology 2010, 11:R88 (26 August 2010) The genome variation format (GVF) and the 10Gen dataset provide a resource for the standardization of variant files and data analysis.
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Research
C André Lévesque, Henk Brouwer, Liliana Cano, John P Hamilton, Carson Holt, Edgar Huitema, Sylvain Raffaele, Gregg P Robideau, Marco Thines, Joe Win, Marcelo M Zerillo, Gordon W Beakes, Jeffrey L Boore, Dana Busam, Bernard Dumas, Steve Ferriera, Susan I Fuerstenberg, Claire MM Gachon, Elodie Gaulin, Francine Govers, Laura Grenville-Briggs, Neil Horner, Jessica Hostetler, Rays HY Jiang, Justin Johnson, Theerapong Krajaejun, Haining Lin, Harold JG Meijer, Barry Moore, Paul Morris et al. Genome Biology 2010, 11:R73 (13 July 2010) The genome sequence of the plant pathogenic oomycete, Pythium ultimum and a comparison with the related potato blight pathogen genome reveals differences in pathogenicity.
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Research article
Chris P Verschoor, Sameer D Pant, Qiumei You, Flavio S Schenkel, David F Kelton, Niel A Karrow BMC Genetics 2010, 11:23 (15 April 2010) |
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Research article
Sarah E London, Yuichiro Itoh, Valentin A Lance, Petra M Wise, Preethika S Ekanayake, Randi K Oyama, Arthur P Arnold, Barney A Schlinger BMC Neuroscience 2010, 11:47 (1 April 2010) This article is part of a collection on Zebra finch: the companion... |
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Research article
Genomic and neural analysis of the estradiol-synthetic pathway in the zebra finch Sarah E London, David F Clayton BMC Neuroscience 2010, 11:46 (1 April 2010) This article is part of a collection on Zebra finch: the companion... Estrogenic steroid-related genes in the zebra finch and other mammals are largely homologous, but steroidogenic enzyme genes might be less diverse in the finch and the neural expression of a cholesterol transport protein gene might be regulated by hearing song.
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Research article
Annotation and classification of the bovine T cell receptor delta genes Carolyn TA Herzig, Marie-Paule Lefranc, Cynthia L Baldwin BMC Genomics 2010, 11:100 (9 February 2010) |
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Software
The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes James C Estill, Jeffrey L Bennetzen Plant Methods 2009, 5:8 (19 June 2009) |
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Research article
Anna Ekman, Mikael Niku, Jenni Liljavirta, Antti Iivanainen BMC Immunology 2009, 10:22 (30 April 2009) This article is part of a collection on Bovine: the companion... |
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Research article
Carolyn TA Herzig, Cynthia L Baldwin BMC Genomics 2009, 10:191 (24 April 2009) This article is part of a collection on Bovine: the companion... |
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Research article
Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies Angela M Walker, R Michael Roberts BMC Genomics 2009, 10:187 (24 April 2009) This article is part of a collection on Bovine: the companion... |
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Research article
Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis Alper Uzun, Nelida Rodriguez-Osorio, Abdullah Kaya, Hongfeng Wang, John J Parrish, Valentin A Ilyin, Erdogan Memili BMC Genomics 2009, 10:183 (24 April 2009) This article is part of a collection on Bovine: the companion... |
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Software
Genome Projector: zoomable genome map with multiple views Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, Masaru Tomita BMC Bioinformatics 2009, 10:31 (23 January 2009) Genome Projector provides an easy-to-use, zoomable and scrollable user interface for browsing of genomic and metabolomic data, utilizing the Google Maps interface, and currently covers 320 bacterial genomes online.
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Software
Automated paleontology of repetitive DNA with RE Vini Pereira BMC Genomics 2008, 9:614 (18 December 2008) |
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Research
Yutaka Satou, Katsuhiko Mineta, Michio Ogasawara, Yasunori Sasakura, Eiichi Shoguchi, Keisuke Ueno, Lixy Yamada, Jun Matsumoto, Jessica Wasserscheid, Ken Dewar, Graham B Wiley, Simone L Macmil, Bruce A Roe, Robert W Zeller, Kenneth EM Hastings, Patrick Lemaire, Erika Lindquist, Toshinori Endo, Kohji Hotta, Kazuo Inaba Genome Biology 2008, 9:R152 (14 October 2008) An improved assembly of the Ciona intestinalis genome reveals that it contains non-canonical introns and that about 20% of Ciona genes reside in operons. |
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Software
GMODWeb: a web framework for the generic model organism database Brian D O'Connor, Allen Day, Scott Cain, Olivier Arnaiz, Linda Sperling, Lincoln D Stein Genome Biology 2008, 9:R102 (20 June 2008) GMODWeb is a software framework designed to speed the development of websites for model organism databases. |
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Software
Jeremy D DeBarry, Renyi Liu, Jeffrey L Bennetzen BMC Bioinformatics 2008, 9:235 (13 May 2008) |
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Software
High-throughput bioinformatics with the Cyrille2 pipeline system Mark WEJ Fiers, Ate van der Burgt, Erwin Datema, Joost CW de Groot, Roeland CHJ van Ham BMC Bioinformatics 2008, 9:96 (12 February 2008) |
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Method
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman Genome Biology 2008, 9:R7 (11 January 2008) EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes. |
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Software
Kathrin Klee, Rebecca Ernst, Manuel Spannagl, Klaus FX Mayer BMC Bioinformatics 2007, 8:320 (30 August 2007) |
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Research
Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome Nunzio D'Agostino, Alessandra Traini, Luigi Frusciante, Maria Chiusano BMC Bioinformatics 2007, 8(Suppl 1):S9 (8 March 2007) |
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Research
Creating a honey bee consensus gene set Christine G Elsik, Aaron J Mackey, Justin T Reese, Natalia V Milshina, David S Roos, George M Weinstock Genome Biology 2007, 8:R13 (22 January 2007) A high-quality consensus gene set for the honey bee ( |
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Database
AgBase: a functional genomics resource for agriculture Fiona M McCarthy, Nan Wang, G Bryce Magee, Bindu Nanduri, Mark L Lawrence, Evelyn B Camon, Daniel G Barrell, David P Hill, Mary E Dolan, W Paul Williams, Dawn S Luthe, Susan M Bridges, Shane C Burgess BMC Genomics 2006, 7:229 (8 September 2006) |
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Software
Matthew D Wilkerson, Shannon D Schlueter, Volker Brendel Genome Biology 2006, 7:R58 (19 July 2006) yrGATE is a new web-based tool for community gene and genome annotation. |
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Research article
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release Brian J Haas, Jennifer R Wortman, Catherine M Ronning, Linda I Hannick, Roger K Smith, Rama Maiti, Agnes P Chan, Chunhui Yu, Maryam Farzad, Dongying Wu, Owen White, Christopher D Town BMC Biology 2005, 3:7 (22 March 2005) The TIGR group explain how they reannotated the Arabidopsis genome, with several thousand new genes and pseudogenes annotated, 1/3 of the original annotations refined and every protein-coding gene assigned to a Gene Ontology term.
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Research article
Molecular characterization of the singed wings locus of Drosophila melanogaster Yuri B Schwartz, Tatiana Boykova, Elena S Belyaeva, Michael Ashburner, Igor F Zhimulev BMC Genetics 2004, 5:15 (9 June 2004) |
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Minireview
Haiqiong Montalta-He, Heinrich Reichert Genome Biology 2003, 4:205 (28 January 2003) The establishment of a database of gene-expression patterns derived from systematic highthroughput |
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Research
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... Annotation of an improved whole-genome shotgun assembly of the |
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Research
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... The recent completion of the |
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Research
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... Analysis of conservation in eight genomic regions ( |
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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, SE Lewis Genome Biology 2002, 3:research0081-0081.11 (23 December 2002) This article is part of a collection on Release 3 of the... In the course of annotating the |
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Research
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... The |