Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (151K) 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 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 arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Li, L.
Right arrow Articles by Roos, D. S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, L.
Right arrow Articles by Roos, D. S.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2004, Vol. 32, Database issue D326-D328
© 2004 Oxford University Press

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites

Li Li, Jonathan Crabtree1, Steve Fischer1, Deborah Pinney1, Christian J. Stoeckert, Jr1, L. David Sibley2 and David S. Roos*

Department of Biology and 1 Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA and 2 Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63108, USA

*To whom correspondence should be addressed. Tel: +1 215 898 2118; Fax: +1 215 898 8780; Email: droos{at}sas.upenn.edu

ApiEST-DB (http://www.cbil.upenn.edu/paradbs-servlet/) provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. The database currently incorporates a total of nearly 100 000 ESTs from several parasite species of clinical and/or veterinary interest, including Eimeria tenella, Neospora caninum, Plasmodium falciparum, Sarcocystis neurona and Toxoplasma gondii. To facilitate analysis of these data, EST sequences were clustered and assembled to form consensus sequences for each organism, and these assemblies were then subjected to automated annotation via similarity searches against protein and domain databases. The underlying relational database infrastructure, Genomics Unified Schema (GUS), enables complex biologically based queries, facilitating validation of gene models, identification of alternative splicing, detection of single nucleotide polymorphisms, identification of stage-specific genes and recognition of phylogenetically conserved and phylogenetically restricted sequences.


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
 Eukaryot CellHome page
J. P. Boyle, J. P. J. Saeij, S. Y. Harada, J. W. Ajioka, and J. C. Boothroyd
Expression Quantitative Trait Locus Mapping of Toxoplasma Genes Reveals Multiple Mechanisms for Strain-Specific Differences in Gene Expression
Eukaryot. Cell, August 1, 2008; 7(8): 1403 - 1414.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. A. O'Brien, L. B. Koski, Y. Zhang, L. Yang, E. Wang, M. W. Gray, G. Burger, and B. F. Lang
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D445 - D451.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Aurrecoechea, M. Heiges, H. Wang, Z. Wang, S. Fischer, P. Rhodes, J. Miller, E. Kraemer, C. J. Stoeckert Jr., D. S. Roos, et al.
ApiDB: integrated resources for the apicomplexan bioinformatics resource center
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D427 - D430.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. P. Boyle, B. Rajasekar, J. P. J. Saeij, J. W. Ajioka, M. Berriman, I. Paulsen, D. S. Roos, L. D. Sibley, M. W. White, and J. C. Boothroyd
Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii
PNAS, July 5, 2006; 103(27): 10514 - 10519.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Heiges, H. Wang, E. Robinson, C. Aurrecoechea, X. Gao, N. Kaluskar, P. Rhodes, S. Wang, C.-Z. He, Y. Su, et al.
CryptoDB: a Cryptosporidium bioinformatics resource update
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D419 - D422.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Aguero, W. Zheng, D. B. Weatherly, P. Mendes, and J. C. Kissinger
TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D428 - D431.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
X. W. Zhou, B. F. C. Kafsack, R. N. Cole, P. Beckett, R. F. Shen, and V. B. Carruthers
The Opportunistic Pathogen Toxoplasma gondii Deploys a Diverse Legion of Invasion and Survival Proteins
J. Biol. Chem., October 7, 2005; 280(40): 34233 - 34244.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Khan, S. Taylor, C. Su, A. J. Mackey, J. Boyle, R. Cole, D. Glover, K. Tang, I. T. Paulsen, M. Berriman, et al.
Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii
Nucleic Acids Res., May 23, 2005; 33(9): 2980 - 2992.
[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.