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This is a list of tools and resources that we have found mentioned in this publication.


UniProt (tool)

RRID:SCR_002380

Collection of data of protein sequence and functional information. UniProt databases are UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc).

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STRING (tool)

RRID:SCR_005223

Database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations and are derived from four sources: Genomic Context, High-throughput experiments, (Conserved) Coexpression, and previous knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers 5''214''234 proteins from 1133 organisms. (2013)

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ApiDB PlasmoDB (tool)

RRID:SCR_013331

PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria. It brings together data provided by numerous laboratories worldwide (see the Data Sources page), and adds its own data analysis. PlasmoDB 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 Bioinformatics Resource Center (BRC) umbrella. PlasmoDB contains numerous 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. Organisms * Annotated genomes: Plasmodium falciparum, Plasmodium vivax, Plasmodium yoelii, Plasmodium berghei, Plasmodium chabaudi, Plasmodium knowlesi * Unannotated genomes: Plasmodium reichenowi, Plasmodium gallinaceum * Others: environmental isolate sequences from numerous species PlasmoDB provides programmatic access to its searches, via REST Web Services.

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EuPathDB - Eukaryotic Pathogen Database Resources (tool)

RRID:SCR_004512

EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with the eukaryotic pathogens (Babesia, Cryptosporidium, Encephalitozoon, Entamoeba, Enterocytozoon, Giardia, Leishmania, Neospora, Plasmodium, Theileria, Toxoplasma, Trichomonas and Trypanosoma). It provides a unified entry point for the Eukaryotic Pathogen integrating AmoebaDB, CryptoDB, GiardiaDB, MicrosporidiaDB, PiroplasmaDB, PlasmoDB, ToxoDB, TrichDB, and TriTrypDB. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. EuPathDB currently supports more than 80 searches and the recently-implemented "search strategy" system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users. EuPathDB provides programmatic access to its searches, via REST Web Services

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