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      AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species

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          Abstract

          AmoebaDB ( http://AmoebaDB.org) and MicrosporidiaDB ( http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species ( E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. The databases belong to the National Institute of Allergy and Infectious Diseases (NIAID) funded EuPathDB ( http://EuPathDB.org) Bioinformatics Resource Center family of integrated databases and assume the same architectural and graphical design as other EuPathDB resources such as PlasmoDB and TriTrypDB. Importantly they utilize the graphical strategy builder that affords a database user the ability to ask complex multi-data-type questions with relative ease and versatility. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user’s profile for future retrieval and may also be shared with other researchers using a unique strategy web address.

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          Most cited references 26

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          PlasmoDB: a functional genomic database for malaria parasites

          PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories—annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.
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            TriTrypDB: a functional genomic resource for the Trypanosomatidae

            TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. ‘User Comments’ may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.
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              Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi.

              Microsporidia are obligate intracellular parasites infesting many animal groups. Lacking mitochondria and peroxysomes, these unicellular eukaryotes were first considered a deeply branching protist lineage that diverged before the endosymbiotic event that led to mitochondria. The discovery of a gene for a mitochondrial-type chaperone combined with molecular phylogenetic data later implied that microsporidia are atypical fungi that lost mitochondria during evolution. Here we report the DNA sequences of the 11 chromosomes of the approximately 2.9-megabase (Mb) genome of Encephalitozoon cuniculi (1,997 potential protein-coding genes). Genome compaction is reflected by reduced intergenic spacers and by the shortness of most putative proteins relative to their eukaryote orthologues. The strong host dependence is illustrated by the lack of genes for some biosynthetic pathways and for the tricarboxylic acid cycle. Phylogenetic analysis lends substantial credit to the fungal affiliation of microsporidia. Because the E. cuniculi genome contains genes related to some mitochondrial functions (for example, Fe-S cluster assembly), we hypothesize that microsporidia have retained a mitochondrion-derived organelle.
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                Author and article information

                Journal
                Nucleic Acids Res
                nar
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                January 2011
                January 2011
                25 October 2010
                25 October 2010
                : 39
                : Database issue , Database issue
                : D612-D619
                Affiliations
                1Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, 2Penn Center for Bioinformatics, University of Pennsylvania, 3Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, 5J. Craig Venter Institute, Rockville, MD 20850, 6Center for Applied Genetic Technologies, 7Department of Genetics and Institute of Bioinformatics and 8Department of Computer Science, University of Georgia, Athens, GA 30602 USA
                Author notes
                *To whom correspondence should be addressed. Tel: +1 215 746 7019; Fax: +1 215 573 3111; Email: oharb@ 123456pcbi.upenn.edu
                Correspondence may also be addressed to Brian P. Brunk. Tel: +1 215 573 3118; Fax: +1 215 573 3111; Email: brunkb@ 123456pcbi.upenn.edu
                Correspondence may also be addressed to Jessica C. Kissinger. Tel: +1 706 542 6562; Fax: +1 706 542 3582; Email: jkissing@ 123456uga.edu
                Correspondence may also be addressed to David S. Roos. Tel: +1 215 898 2118; Fax: +1 215 746 6697; Email: droos@ 123456sas.upenn.edu
                Correspondence may also be addressed to Christian J. Stoeckert Jr. Tel: +1 215 573 4409; Fax: +1 215 573 3111; Email: stoeckrt@ 123456pcbi.upenn.edu
                Article
                gkq1006
                10.1093/nar/gkq1006
                3013638
                20974635
                © The Author(s) 2010. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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