Genome Biology

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Full-length messenger RNA sequences greatly improve genome annotation

Brian J Haas, Natalia Volfovsky, Christopher D Town, Maxim Troukhan, Nickolai Alexandrov, Kenneth A Feldmann, Richard B Flavell, Owen White and Steven L Salzberg*

Genome Biology 2002, 3:research0029-research0029.12 doi:10.1186/gb-2002-3-6-research0029

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Research article   Open Access

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)

Research article   Open Access Highly Accessed

Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana

Xiaoping Gou, Kai He, Hui Yang, Tong Yuan, Honghui Lin, Steven D Clouse, Jia Li BMC Genomics 2010, 11:19 (11 January 2010)

Research article   Open Access

A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus

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)

Research   Open Access

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)

Method   Open Access Highly Accessed

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

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.

Software   Open Access

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)

Research article   Open Access

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana

Mihaela Pertea, Stephen M Mount, Steven L Salzberg BMC Bioinformatics 2007, 8:159 (21 May 2007)

Research   Open Access

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)

Research article   Open Access

Experimental validation of novel genes predicted in the un-annotated regions of the Arabidopsis genome

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)

Research article   Open Access

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.

Research article   Open Access

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.

Research article   Open Access

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)

Research   Open Access Highly Accessed

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 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.

Research   Open Access Highly Accessed

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...

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.

Software   Open Access Highly Accessed

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 Drosophila melanogaster genome.

Software   Open Access Highly Accessed

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 Drosophila melanogaster genome sequence, several new open-source software tools and a database schema to support large-scale genome annotation were developed and integrated in to a reusable software system for whole-genome annotation.

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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 Drosophila genes by aligning 5' expressed sequence tags (ESTs) from cap-trapped cDNA libraries to the genome. Examination of the sequences flanking these candidate transcription start sites revealed the presence of well-known core promoter motifs such as the TATA box, the initiator and the downstream promoter element (DPE).