Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (518K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (77)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Haas, B. J.
Right arrow Articles by White, O.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Haas, B. J.
Right arrow Articles by White, O.
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 19 5654-5666
© 2003 Oxford University Press

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

Brian J. Haas*, Arthur L. Delcher, Stephen M. Mount1, Jennifer R. Wortman, Roger K. Smith Jr, Linda I. Hannick, Rama Maiti, Catherine M. Ronning, Douglas B. Rusch2, Christopher D. Town, Steven L. Salzberg and Owen White

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA, 1 Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA and 2 The Center for Advancement of Genomics, 1901 Research Boulevard, Rockville, MD 20850, USA

*To whom correspondence should be addressed. Tel: +1 301 610 5988; Fax: +1 301 838 0208; Email: bhaas{at}tigr.org

The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the ~27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
M. Stanke, M. Diekhans, R. Baertsch, and D. Haussler
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Bioinformatics, March 1, 2008; 24(5): 637 - 644.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Swarbreck, C. Wilks, P. Lamesch, T. Z. Berardini, M. Garcia-Hernandez, H. Foerster, D. Li, T. Meyer, R. Muller, L. Ploetz, et al.
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D1009 - D1014.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
A. Siepel, M. Diekhans, B. Brejova, L. Langton, M. Stevens, C. L.G. Comstock, C. Davis, B. Ewing, S. Oommen, C. Lau, et al.
Targeted discovery of novel human exons by comparative genomics
Genome Res., December 1, 2007; 17(12): 1763 - 1773.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
S. Balasenthil, A. E. Gururaj, A. H. Talukder, R. Bagheri-Yarmand, T. Arrington, B. J. Haas, J. C. Braisted, I. Kim, N. H. Lee, and R. Kumar
Identification of Pax5 as a Target of MTA1 in B-Cell Lymphomas
Cancer Res., August 1, 2007; 67(15): 7132 - 7138.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
S. Sato, Y. Nakamura, E. Asamizu, S. Isobe, and S. Tabata
Genome Sequencing and Genome Resources in Model Legumes
Plant Physiology, June 1, 2007; 144(2): 588 - 593.
[Full Text] [PDF]

Home page
 Genome Res.Home page
W. Zhu and C. R. Buell
Improvement of whole-genome annotation of cereals through comparative analyses
Genome Res., March 1, 2007; 17(3): 299 - 310.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Ouyang, W. Zhu, J. Hamilton, H. Lin, M. Campbell, K. Childs, F. Thibaud-Nissen, R. L. Malek, Y. Lee, L. Zheng, et al.
The TIGR Rice Genome Annotation Resource: improvements and new features
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D883 - D887.
[Abstract] [Full Text] [PDF]

Home page
 SIMHome page
A. Rokas, G. Payne, N.D. Fedorova, S.E. Baker, M. Machida, J. Yu, D. R. Georgianna, R. A. Dean, D. Bhatnagar, T.E. Cleveland, et al.
What can comparative genomics tell us about species concepts in the genus Aspergillus?
Stud Mycol, January 1, 2007; 59(1): 11 - 17.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Xing, T. Yu, Y. N. Wu, M. Roy, J. Kim, and C. Lee
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs
Nucleic Acids Res., June 6, 2006; 34(10): 3150 - 3160.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
G. Thill, V. Castelli, S. Pallud, M. Salanoubat, P. Wincker, P. de la Grange, D. Auboeuf, V. Schachter, and J. Weissenbach
ASEtrap: A biological method for speeding up the exploration of spliceomes
Genome Res., June 1, 2006; 16(6): 776 - 786.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
B.-B. Wang and V. Brendel
Genomewide comparative analysis of alternative splicing in plants
PNAS, May 2, 2006; 103(18): 7175 - 7180.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
L. Florea
Bioinformatics of alternative splicing and its regulation
Brief Bioinform, March 1, 2006; 7(1): 55 - 69.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
H. Ner-Gaon and R. Fluhr
Whole-Genome Microarray in Arabidopsis Facilitates Global Analysis of Retained Introns
DNA Res, January 1, 2006; 13(3): 111 - 121.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
Y.-L. Xiao, S. R. Smith, N. Ishmael, J. C. Redman, N. Kumar, E. L. Monaghan, M. Ayele, B. J. Haas, H. C. Wu, and C. D. Town
Analysis of the cDNAs of Hypothetical Genes on Arabidopsis Chromosome 2 Reveals Numerous Transcript Variants
Plant Physiology, November 1, 2005; 139(3): 1323 - 1337.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
The Rice Chromosome 3 Sequencing Consortium
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
Genome Res., September 1, 2005; 15(9): 1284 - 1291.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
J. C. Loke, E. A. Stahlberg, D. G. Strenski, B. J. Haas, P. C. Wood, and Q. Q. Li
Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures
Plant Physiology, July 1, 2005; 138(3): 1457 - 1468.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
A. A. Sharov, D. B. Dudekula, and M. S.H. Ko
Genome-wide assembly and analysis of alternative transcripts in mouse
Genome Res., May 1, 2005; 15(5): 748 - 754.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. D. Wu and C. K. Watanabe
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics, May 1, 2005; 21(9): 1859 - 1875.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
Q. Yuan, S. Ouyang, A. Wang, W. Zhu, R. Maiti, H. Lin, J. Hamilton, B. Haas, R. Sultana, F. Cheung, et al.
The Institute for Genomic Research Osa1 Rice Genome Annotation Database
Plant Physiology, May 1, 2005; 138(1): 18 - 26.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
S. B. Cannon, J. A. Crow, M. L. Heuer, X. Wang, E. K.S. Cannon, C. Dwan, A.-F. Lamblin, J. Vasdewani, J. Mudge, A. Cook, et al.
Databases and Information Integration for the Medicago truncatula Genome and Transcriptome
Plant Physiology, May 1, 2005; 138(1): 38 - 46.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
M. Ayele, B. J. Haas, N. Kumar, H. Wu, Y. Xiao, S. Van Aken, T. R. Utterback, J. R. Wortman, O. R. White, and C. D. Town
Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
Genome Res., April 1, 2005; 15(4): 487 - 495.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
M. S. Katari, V. Balija, R. K. Wilson, R. A. Martienssen, and W. R. McCombie
Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana
Genome Res., April 1, 2005; 15(4): 496 - 504.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
L. Florea, V. Di Francesco, J. Miller, R. Turner, A. Yao, M. Harris, B. Walenz, C. Mobarry, G. V. Merkulov, R. Charlab, et al.
Gene and alternative splicing annotation with AIR
Genome Res., January 1, 2005; 15(1): 54 - 66.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Aubourg, V. Brunaud, C. Bruyere, M. Cock, R. Cooke, A. Cottet, A. Couloux, P. Dehais, G. Deleage, A. Duclert, et al.
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D641 - D646.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
S. J. Robinson, D. J. Cram, C. T. Lewis, and I. A.P. Parkin
Maximizing the Efficacy of SAGE Analysis Identifies Novel Transcripts in Arabidopsis
Plant Physiology, October 1, 2004; 136(2): 3223 - 3233.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Iida, M. Seki, T. Sakurai, M. Satou, K. Akiyama, T. Toyoda, A. Konagaya, and K. Shinozaki
Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences
Nucleic Acids Res., September 27, 2004; 32(17): 5096 - 5103.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
N. Suzuki, Y. Nakano, A. Yoshida, Y. Yamashita, and Y. Kiyoura
Real-Time TaqMan PCR for Quantifying Oral Bacteria during Biofilm Formation
J. Clin. Microbiol., August 1, 2004; 42(8): 3827 - 3830.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
R. Sorek, R. Shemesh, Y. Cohen, O. Basechess, G. Ast, and R. Shamir
A Non-EST-Based Method for Exon-Skipping Prediction
Genome Res., August 1, 2004; 14(8): 1617 - 1623.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
B. C. Meyers, S. S. Tej, T. H. Vu, C. D. Haudenschild, V. Agrawal, S. B. Edberg, H. Ghazal, and S. Decola
The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis
Genome Res., August 1, 2004; 14(8): 1641 - 1653.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
W.A. Rensink and C. R. Buell
Arabidopsis to Rice. Applying Knowledge from a Weed to Enhance Our Understanding of a Crop Species
Plant Physiology, June 1, 2004; 135(2): 622 - 629.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
B. C. Meyers, D. K. Lee, T. H. Vu, S. S. Tej, S. B. Edberg, M. Matvienko, and L. D. Tindell
Arabidopsis MPSS. An Online Resource for Quantitative Expression Analysis
Plant Physiology, June 1, 2004; 135(2): 801 - 813.
[Full Text] [PDF]

Home page
 Plant Physiol.Home page
B. C. Meyers, D. W. Galbraith, T. Nelson, and V. Agrawal
Methods for Transcriptional Profiling in Plants. Be Fruitful and Replicate
Plant Physiology, June 1, 2004; 135(2): 637 - 652.
[Full Text] [PDF]

Home page
 Genome Res.Home page
V. Castelli, J.-M. Aury, O. Jaillon, P. Wincker, C. Clepet, M. Menard, C. Cruaud, F. Quetier, C. Scarpelli, V. Schachter, et al.
Whole Genome Sequence Comparisons and "Full-Length" cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation
Genome Res., March 1, 2004; 14(3): 406 - 413.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.