Abstract
Over the past 20 years, advances in high-throughput biological techniques and the availability of computational resources including fast Internet access have resulted in an explosion of large genome-scale data sets “big data.” While such data are readily available for download and personal use and analysis from a variety of repositories, often such analysis requires access to seldom-available computational skills. As a result a number of databases have emerged to provide scientists with online tools enabling the interrogation of data without the need for sophisticated computational skills beyond basic knowledge of Internet browser utility. This chapter focuses on the Eukaryotic Pathogen Databases (EuPathDB: http://eupathdb.org) Bioinformatic Resource Center (BRC) and illustrates some of the available tools and methods.
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References
Aurrecoechea C, Brestelli J, Brunk BP et al (2010) EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res 38:D415–9. doi:10.1093/nar/gkp941
Aslett M, Aurrecoechea C, Berriman M et al (2009) TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res 38:D457–D462. doi:10.1093/nar/gkp851
Logan-Klumpler FJ, De Silva N, Boehme U et al (2012) GeneDB—an annotation database for pathogens. Nucleic Acids Res 40:D98–108. doi:10.1093/nar/gkr1032
Fischer S, Aurrecoechea C, Brunk BP, et al. (2011) The strategies WDK: a graphical search interface and web development kit for functional genomics databases. Database (Oxford) 2011:bar027. doi: 10.1093/database/bar027
Stajich JE, Harris T, Brunk BP et al (2012) FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res 40:D675–81. doi:10.1093/nar/gkr918
Zerlotini A, Heiges M, Wang H et al (2009) SchistoDB: a Schistosoma mansoni genome resource. Nucleic Acids Res 37:D579–82. doi:10.1093/nar/gkn681
Galagan JE, Sisk P, Stolte C et al (2010) TB database 2010: overview and update. Tuberculosis (Edinb) 90:225–235. doi:10.1016/j.tube.2010.03.010
Mazzarelli JM, Brestelli J, Gorski RK et al (2007) EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. Nucleic Acids Res 35:D751–5. doi:10.1093/nar/gkl748
Tarun AS, Peng X, Dumpit RF et al (2008) A combined transcriptome and proteome survey of malaria parasite liver stages. Proc Natl Acad Sci 105:305–310. doi:10.1073/pnas.0710780104
Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189. doi:10.1101/gr.1224503
Chen F, Mackey AJ, Stoeckert CJ, Roos DS (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 34:D363–8. doi:10.1093/nar/gkj123
Fischer S, Brunk BP, Chen F, et al. (2011) Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics 1–19 Chapter 6:Unit 6.12.1–19
Tetteh KKA, Stewart LB, Ochola LI et al (2009) Prospective identification of malaria parasite genes under balancing selection. PLoS One 4:e5568. doi:10.1371/journal.pone.0005568
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Harb, O.S., Roos, D.S. (2015). The Eukaryotic Pathogen Databases: A Functional Genomic Resource Integrating Data from Human and Veterinary Parasites. In: Peacock, C. (eds) Parasite Genomics Protocols. Methods in Molecular Biology, vol 1201. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1438-8_1
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DOI: https://doi.org/10.1007/978-1-4939-1438-8_1
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