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Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Morrison HG, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ, Sullivan S, Treatman C, Wang H. GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res 2009; 37:D526-30. [PMID: 18824479 PMCID: PMC2686445 DOI: 10.1093/nar/gkn631] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 09/14/2008] [Indexed: 12/03/2022] Open
Abstract
GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.
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Affiliation(s)
- Cristina Aurrecoechea
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - John Brestelli
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Brian P. Brunk
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Jane M. Carlton
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Jennifer Dommer
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Steve Fischer
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Bindu Gajria
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Xin Gao
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Alan Gingle
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Greg Grant
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Omar S. Harb
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Mark Heiges
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Frank Innamorato
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - John Iodice
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Jessica C. Kissinger
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Eileen Kraemer
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Wei Li
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - John A. Miller
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Hilary G. Morrison
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Vishal Nayak
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Cary Pennington
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Deborah F. Pinney
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - David S. Roos
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Chris Ross
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Christian J. Stoeckert
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Steven Sullivan
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Charles Treatman
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Haiming Wang
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, Department of Medical Parasitology, New York University Langone Medical Center, New York, NY 10010, Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, Department of Genetics, Department of Computer Science, University of Georgia, Athens, GA 30602, Josephine Bay Paul Center [for Comparative Molecular Biology and Evolution], Marine Biological Laboratory, Woods Hole, MA 02543 and Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
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