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AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
Mario Stanke, Ana Tzvetkova, Burkhard Morgenstern
Genome Biol. 2006; 7(Suppl 1): S11. Published online 2006 August 7. doi: 10.1186/gb-2006-7-s1-s11
PMCID:
PMC1810548
Abstract Full Text PDF–541K

Is Cited by the Following 9 Articles in this Archive:

Transcriptomic Responses of the Softwood-Degrading White-Rot Fungus Phanerochaete carnosa during Growth on Coniferous and Deciduous Wood
Jacqueline MacDonald, Matt Doering, Thomas Canam, Yunchen Gong, David S. Guttman, Malcolm M. Campbell, Emma R. Master
Appl Environ Microbiol. 2011 May; 77(10): 3211–3218. doi: 10.1128/AEM.02490-10
PMCID:
PMC3126436
Abstract Full Text PDF–1.4M Supplementary Material
The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle
Garret Suen, Clotilde Teiling, Lewyn Li, Carson Holt, Ehab Abouheif, Erich Bornberg-Bauer, Pascal Bouffard, Eric J. Caldera, Elizabeth Cash, Amy Cavanaugh, Olgert Denas, Eran Elhaik, Marie-Julie Favé, Jürgen Gadau, Joshua D. Gibson, Dan Graur, Kirk J. Grubbs, Darren E. Hagen, Timothy T. Harkins, Martin Helmkampf, Hao Hu, Brian R. Johnson, Jay Kim, Sarah E. Marsh, Joseph A. Moeller, Mónica C. Muñoz-Torres, Marguerite C. Murphy, Meredith C. Naughton, Surabhi Nigam, Rick Overson, Rajendhran Rajakumar, Justin T. Reese, Jarrod J. Scott, Chris R. Smith, Shu Tao, Neil D. Tsutsui, Lumi Viljakainen, Lothar Wissler, Mark D. Yandell, Fabian Zimmer, James Taylor, Steven C. Slater, Sandra W. Clifton, Wesley C. Warren, Christine G. Elsik, Christopher D. Smith, George M. Weinstock, Nicole M. Gerardo, Cameron R. Currie
PLoS Genet. 2011 February; 7(2): e1002007. Published online 2011 February 10. doi: 10.1371/journal.pgen.1002007
PMCID:
PMC3037820
Abstract Full Text PDF–685K Supplementary Material
The Amphimedon queenslandica genome and the evolution of animal complexity
Mansi Srivastava, Oleg Simakov, Jarrod Chapman, Bryony Fahey, Marie E. A. Gauthier, Therese Mitros, Gemma S. Richards, Cecilia Conaco, Michael Dacre, Uffe Hellsten, Claire Larroux, Nicholas H. Putnam, Mario Stanke, Maja Adamska, Aaron Darling, Sandie M. Degnan, Todd H. Oakley, David C. Plachetzki, Yufeng Zhai, Marcin Adamski, Andrew Calcino, Scott F. Cummins, David M. Goodstein, Christina Harris, Daniel J. Jackson, Sally P. Leys, Shengqiang Shu, Ben J. Woodcroft, Michel Vervoort, Kenneth S. Kosik, Gerard Manning, Bernard M. Degnan, Daniel S. Rokhsar
Nature. Author manuscript; available in PMC 2011 July 6.
Published in final edited form as: Nature. 2010 August 5; 466(7307): 720–726. doi: 10.1038/nature09201
PMCID:
PMC3130542
Abstract Full Text PDF–3.1M Supplementary Material
EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data
Ernesto Picardi, Flavio Mignone, Graziano Pesole
BMC Bioinformatics. 2009; 10(Suppl 6): S10. Published online 2009 June 16. doi: 10.1186/1471-2105-10-S6-S10
PMCID:
PMC2697633
Abstract Full Text PDF–336K
Reranking candidate gene models with cross-species comparison for improved gene prediction
Qian Liu, Koby Crammer, Fernando CN Pereira, David S Roos
BMC Bioinformatics. 2008; 9: 433. Published online 2008 October 14. doi: 10.1186/1471-2105-9-433
PMCID:
PMC2587481
Abstract Full Text PDF–678K
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
Amarendran R Subramanian, Michael Kaufmann, Burkhard Morgenstern
Algorithms Mol Biol. 2008; 3: 6. Published online 2008 May 27. doi: 10.1186/1748-7188-3-6
PMCID:
PMC2430965
Abstract Full Text PDF–296K
MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes
Brandi L. Cantarel, Ian Korf, Sofia M.C. Robb, Genis Parra, Eric Ross, Barry Moore, Carson Holt, Alejandro Sánchez Alvarado, Mark Yandell
Genome Res. 2008 January; 18(1): 188–196. doi: 10.1101/gr.6743907
PMCID:
PMC2134774
Abstract Full Text PDF–410K
Conrad: Gene prediction using conditional random fields
David DeCaprio, Jade P. Vinson, Matthew D. Pearson, Philip Montgomery, Matthew Doherty, James E. Galagan
Genome Res. 2007 September; 17(9): 1389–1398. doi: 10.1101/gr.6558107
PMCID:
PMC1950907
Abstract Full Text PDF–469K
EGASP: the human ENCODE Genome Annotation Assessment Project
Roderic Guigó, Paul Flicek, Josep F Abril, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E Lewis, Martin G Reese
Genome Biol. 2006; 7(Suppl 1): S2. Published online 2006 August 7. doi: 10.1186/gb-2006-7-s1-s2
PMCID:
PMC1810551
Abstract Full Text PDF–2.1M
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