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VarDom 1.0 Server

This server is dedicated to composition and classification analysis of the malaria antigen family Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1).

BROWSE DATABASE

Browse the database consisting of PfEMP1 from seven P. falciparum genomes (3D7, DD2, HB3, IT4, PFCLIN, IGH, RAJ116) and related proteins (see reference below for details).

Press submit to see all proteins with all homology blocks, or filter output by filling one or more fields below.

Protein display filter
 
Protein IDs (part or whole ID, comma separated)

Example: PFL0030c,HB3,REICH   (write 3D7 to see all PfEMP1 from the 3D7 genome)
 
AND
Homology blocks (exact name or number, comma separated)

Example: 255,341,295   (To get HB11 just submit: 11)
 
AND
UPS-group (part or whole group-name, comma separated)

Example: UPSA,UPSE   (NOTE queries are case sensitive)
 
AND
Phylogenetic domain class (exact class-names, comma separated)

Example: NTSA1,DBLg12   (NOTE queries are case sensitive)
 
Homology block display filter

only show these HBs (exact name or number, comma separated)

Example: 11,13


Proteins per result page  


 

DOMAIN AND HOMOLOGY BLOCK PREDICTION

Submit your protein sequences for prediction of PfEMP1 domains and homology blocks.

Paste a single sequence or several sequences in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

Lower bit-score threshold for homology blocks   
(default is gathering cut-off = 9.97)

Restrictions:
At most 2000 sequences per submission; each sequence not more than 10,000 amino acids.
Total number of amino acids can not exceed 400,000.

Confidentiality:
The sequences are kept confidential and will be deleted after processing.


CITATIONS

For publication of results, please cite:

Plasmodium falciparum erythrocyte membrane protein 1 diversity in seven genomes - divide and conquer
Rask TS, Hansen DA, Theander TG, Gorm Pedersen A, Lavstsen T
PLoS Computational Biology 2010 Sep;6(9). pii: e1000933. link



GETTING HELP

Scientific problems:        Technical problems: