PlasmoDB: a functional genomic database for malaria parasites

By C. Aurrecoechea, John Brestelli, Brian P. Brunk, Jennifer Dommer, S. Fischer, Bindu Gajria, Xin Gao, A. Gingle, Gregory R. Grant, O. Harb and 15 more. Nucleic Acids Res., 2008

1,194 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/f5f4a0933cf097fb14ab84ca295b1bdfe01f97e0

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Citations in the corpus

Structural and Biochemical Characterization of Plasmodium falciparum 12 (Pf12) Reveals a Unique Interdomain Organization and the Potential for an Antiparallel Arrangement with Pf41* (2013, methodology): “Polymorphism and Phylogenetic Analyses—6-Cys protein family member DNA sequences and strain-specific single nucleotide polymorphisms (SNPs) were downloaded from GenBank and PlasmoDB (13 isolates) (28) to calculate the ratio of synonymous to non-synonymous changes.”
Structure of the Pf12 and Pf41 heterodimeric complex of Plasmodium falciparum 6-cysteine proteins (2022, background): “…parasite in humans, the 6-cys family has 14 members, Pfs230, Pfs48/45, Pf230p, PfP47, PfSOP12, Pf52, Pf36, PfLISP2, PfB9, Pf12, P12p, Pf41, Pf38, and Pf92, that are conserved across Plasmodium species and expressed throughout the life cycle in a stage-specific manner (Aurrecoechea et al. 2009).”
Structure of the Plasmodium 6-cysteine s48/45 domain (2012, background): “23. VanBuskirk KM, et al. (2009) Preerythrocytic, live-attenuated Plasmodium falciparum”
The Immune Epitope Database (IEDB): 2018 update (2018, methodology): “We plan to develop more complex ontology modelling of our data and have been testing these principles via an early stage triple store that presents IEDB data alongside that of related resources ImmPort (18) and PlasmoDB (19), allowing federated queries across the combined dataset.”
Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes (2012, background): “%) and a 540 bp locus (Pf3D7_11:1294982-1295521) with a relatively balanced base composition (positive control) from the P. falciparum 3D7 genome http://www.plas-modb.org [8].”
The s48/45 six-cysteine proteins: mediators of interaction throughout the Plasmodium life cycle (2016, background): “with most of the members having orthologues in human, non-human primate and rodent malaria parasites (PlamoDB (Aurrecoechea et al., 2009), attesting to the universal importance of the 6-cys family in survival and propagation of Plasmodium.”
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis (2009, background): “shtml), 3 from VectorBase (15), 2 from PlasmoDB (16) and 2 from CryptoDB (17).”