- Plasmodium domain architectures
- CLADE is the domain prediction tool used in plasmobase, the CLADE package can be downloaded here .
- DAMA is the tool used to resolve domain architectures, the DAMA package can be downloaded here
Plasmobase downloadable xls files contain the full list of annotations for the 11 Plasmodium species.
Each file contains, for each domain hit:
- PlasmoDB accession number of the sequence where the hit is identified
- the Pfam domain name
- the Pfam accession number
- the E-value
- CLADE SVM probability
- the model identifier in the CLADE model library (either a clade-centered model or a Pfam consensus model)
- the start and the end position of the hit either in the domain sequence used to construct the clade-centered model or in the Pfam consensus model
- the clade name (if any)
- the organism name of the sequence originating the clade-centered model used for the domain identification.
Note that if a protein sequence is annotated by several domains, the file contains several rows, one for each domain annotation.
Plasmodium falciparum 3D7
Plasmodium falciparum IT
Plasmodium vivax Sal-1
Plasmodium berghei ANKA
Plasmodium yoelii yoelii 17X
Plasmodium yoelii yoelii 17XNL
Plasmodium yoelii yoelii YM
Plasmodium chabaudi chabaudi
Plasmodium cynomolgi B
Plasmodium knowlesi H
Plasmodium reichenowi CDC