Full-length messenger RNA sequences greatly improve genome annotation
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* Corresponding author: Steven L Salzberg salzberg@tigr.org
Genome Biology 2002, 3:research0029-research0029.12 doi:10.1186/gb-2002-3-6-research0029
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Identification and analysis of in planta expressed genes of Magnaporthe oryzae Soonok Kim, Jongsun Park, Sook-Young Park, Thomas K Mitchell, Yong-Hwan Lee BMC Genomics 2010, 11:104 (10 February 2010) |
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Xiaoping Gou, Kai He, Hui Yang, Tong Yuan, Honghui Lin, Steven D Clouse, Jia Li BMC Genomics 2010, 11:19 (11 January 2010) |
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M Carmen Marques, Hugo Alonso-Cantabrana, Javier Forment, Raquel Arribas, Santiago Alamar, Vicente Conejero, Miguel A Perez-Amador BMC Genomics 2009, 10:428 (11 September 2009) |
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Splign: algorithms for computing spliced alignments with identification of paralogs Yuri Kapustin, Alexander Souvorov, Tatiana Tatusova, David Lipman Biology Direct 2008, 3:20 (21 May 2008) |
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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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EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome Françoise Thibaud-Nissen, Matthew Campbell, John P Hamilton, Wei Zhu, C Buell BMC Genomics 2007, 8:388 (25 October 2007) |
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Mihaela Pertea, Stephen M Mount, Steven L Salzberg BMC Bioinformatics 2007, 8:159 (21 May 2007) |
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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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William A Moskal, Hank C Wu, Beverly A Underwood, Wei Wang, Christopher D Town, Yongli Xiao BMC Genomics 2007, 8:18 (17 January 2007) |
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Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis Matthew A Campbell, Brian J Haas, John P Hamilton, Stephen M Mount, C Robin Buell BMC Genomics 2006, 7:327 (28 December 2006) |
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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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Widespread presence of "bacterial-like" PPP phosphatases in eukaryotes Alexandra V Andreeva, Mikhail A Kutuzov BMC Evolutionary Biology 2004, 4:47 (19 November 2004) In addition to "conventional" eukaryotic PPP serine/threonine-specific protein phosphatases, many eukaryotes possess very diverse "bacterial-like" PPP phosphatases.
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Formin homology 2 domains occur in multiple contexts in angiosperms Fatima Cvrčková, Marian Novotný, Denisa Pícková, Viktor Žárský BMC Genomics 2004, 5:44 (15 July 2004) |
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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... The recent completion of the |
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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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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... Apollo was developed to enable curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the |
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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, 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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Computational analysis of core promoters in the Drosophila genome Uwe Ohler, Guo-chun Liao, Heinrich Niemann, Gerald M Rubin Genome Biology 2002, 3:research0087-0087.12 (20 December 2002) This article is part of a collection on Release 3 of the... Candidate transcription start sites have been identified for about 2,000 |