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VarDom - 1.0

Domains in the malaria antigen family PfEMP1

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

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

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


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

If you need help regarding technical issues (e.g. errors or missing results) contact Technical Support. Please include the name of the service and version (e.g. NetPhos-4.0). If the error occurs after the job has started running, please include the JOB ID (the long code that you see while the job is running).

If you have scientific questions (e.g. how the method works or how to interpret results), contact Correspondence.

Correspondence: Technical Support: