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Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, Crouch K, Doherty R, Falke D, Fischer S, Gajria B, Harb OS, Heiges M, Hertz-Fowler C, Hu S, Iodice J, Kissinger JC, Lawrence C, Li W, Pinney DF, Pulman JA, Roos DS, Shanmugasundram A, Silva-Franco F, Steinbiss S, Stoeckert CJ, Spruill D, Wang H, Warrenfeltz S, Zheng J. EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Res 2016; 45:D581-D591. [PMID: 27903906 PMCID: PMC5210576 DOI: 10.1093/nar/gkw1105] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 10/28/2016] [Indexed: 12/26/2022] Open
Abstract
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions.
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Affiliation(s)
- Cristina Aurrecoechea
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Ana Barreto
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evelina Y Basenko
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - John Brestelli
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian P Brunk
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shon Cade
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Crouch
- Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow G12 8TA, UK
| | - Ryan Doherty
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dave Falke
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Steve Fischer
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bindu Gajria
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Omar S Harb
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA .,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark Heiges
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | | | - Sufen Hu
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Iodice
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica C Kissinger
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Cris Lawrence
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wei Li
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Deborah F Pinney
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jane A Pulman
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David S Roos
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Achchuthan Shanmugasundram
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Fatima Silva-Franco
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Sascha Steinbiss
- Wellcome Trust Sanger Institute, Parasite Genomics, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Christian J Stoeckert
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Drew Spruill
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Haiming Wang
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Susanne Warrenfeltz
- Center for Tropical & Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Jie Zheng
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C, Berriman M, Otto TD. Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Res 2016; 44:W29-34. [PMID: 27105845 PMCID: PMC4987884 DOI: 10.1093/nar/gkw292] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/08/2016] [Indexed: 01/25/2023] Open
Abstract
Currently available sequencing technologies enable quick and economical sequencing of many new eukaryotic parasite (apicomplexan or kinetoplastid) species or strains. Compared to SNP calling approaches, de novo assembly of these genomes enables researchers to additionally determine insertion, deletion and recombination events as well as to detect complex sequence diversity, such as that seen in variable multigene families. However, there currently are no automated eukaryotic annotation pipelines offering the required range of results to facilitate such analyses. A suitable pipeline needs to perform evidence-supported gene finding as well as functional annotation and pseudogene detection up to the generation of output ready to be submitted to a public database. Moreover, no current tool includes quick yet informative comparative analyses and a first pass visualization of both annotation and analysis results. To overcome those needs we have developed the Companion web server (http://companion.sanger.ac.uk) providing parasite genome annotation as a service using a reference-based approach. We demonstrate the use and performance of Companion by annotating two Leishmania and Plasmodium genomes as typical parasite cases and evaluate the results compared to manually annotated references.
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Affiliation(s)
- Sascha Steinbiss
- Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Fatima Silva-Franco
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Brian Brunk
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bernardo Foth
- Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Matthew Berriman
- Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Thomas D Otto
- Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MAJ, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PAM, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AGM, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Res 2014; 43:D637-44. [PMID: 25300491 PMCID: PMC4384016 DOI: 10.1093/nar/gku944] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.
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Affiliation(s)
- Sanu Shameer
- Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | | | - Florence Vinson
- Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | - Ludovic Cottret
- Institut National de la Recherche Agronomique (INRA), UMR441, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Auzeville, France
| | - Benjamin Merlet
- Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | - Fiona Achcar
- University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
| | - Michael Boshart
- Ludwig-Maximilians-Universität München, Biocenter, 82152-Martinsried, Germany
| | - Matthew Berriman
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | | | | | | | | | - Darren J Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | | | | | - Hubert Denise
- European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | | | | | | | - Michael L Ginger
- Divisionof Biomedical and Life Sciences, Lancaster University, Bailrigg, Lancaster, LA1 4YG, UK
| | | | - Eduard J Kerkhoven
- Chalmers University of Technology, Kemivägen 10, 412 96, Göteborg, Sweden
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Socinstr. 57, Basel 4051, Switzerland
| | | | - Archana Nayak
- University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
| | | | | | | | | | - Terry K Smith
- University of St Andrews, St Andrews, Scotland, KY16 9ST, UK
| | | | - Aloysius G M Tielens
- Utrecht University, Utrecht, 3508 TD, The Netherlands Erasmus University Medical Center, Rotterdam, 3015 CE, The Netherlands
| | - Michael D Urbaniak
- Divisionof Biomedical and Life Sciences, Lancaster University, Bailrigg, Lancaster, LA1 4YG, UK
| | | | | | | | - Susan Wyllie
- University of Dundee, Dundee, Scotland, DD1 4HN, UK
| | | | | | - Fabien Jourdan
- Institut National de la Recherche Agronomique (INRA), UMR1331, TOXALIM (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
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