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OrthoMCL: identification of ortholog groups for eukaryotic genomes.
TLDR
OrthoMCL provides a scalable method for constructing orthologous groups across multiple eukaryotic taxa, using a Markov Cluster algorithm to group (putative) orthologs and paralogs.
Genome sequence of the human malaria parasite Plasmodium falciparum
TLDR
The genome sequence of P. falciparum clone 3D7 is reported, which is the most (A + T)-rich genome sequenced to date and is being exploited in the search for new drugs and vaccines to fight malaria.
PlasmoDB: a functional genomic database for malaria parasites
TLDR
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.
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
TLDR
The OrthoMCL-DB provides a centralized warehouse for orthology prediction among multiple species, and will be updated and expanded as additional genome sequence data become available.
TriTrypDB: a functional genomic resource for the Trypanosomatidae
TLDR
TriTrypDB 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, utilizing a sophisticated search strategy system.
Molecular tools for genetic dissection of the protozoan parasite Toxoplasma gondii.
TLDR
This chapter outlines the use of several of the molecular genetic tools that have recently been developed for the T. gondii system, which provide a powerful arsenal for investigations into the biology of intracellular parasitism.
ToxoDB: an integrated Toxoplasma gondii database resource
TLDR
ToxoDB has matured significantly since its initial release and the numerous updates with respect to the data and increased functionality available on the website are outlined.
A Plastid of Probable Green Algal Origin in Apicomplexan Parasites
TLDR
Observations indicate that the Apicomplexa acquired a plastid by secondary endosymbiosis, probably from a green alga.
Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.
TLDR
This work describes how you can group your proteins of interest into ortholog clusters using two different means provided by the OrthoMCL system.
Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum.
TLDR
This work has identified nuclear genes encoding ribosomal proteins S9 and L28 and the fatty acid biosynthetic enzymes acyl carrier protein (ACP), beta-ketoacyl-ACP synthase III (FabH), and beta-hydroxyacyL-ACP dehydratase (FabZ) that are potentially an excellent target for therapeutics directed against malaria, toxoplasmosis, and other apicomplexan-mediated diseases.
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