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 Tools    >>PVS

 Protein Variability Server  

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If you have found this resource useful for your research, please, tell about it to the SECRETARIA GENERAL DE CIENCIA, TECNOLOGIA E INNOVACION OF SPAIN (sgcti@mineco.es, dgi@mineco.es).This site is in danger and we count on your help to keep it up and running. Thanks.

User Guide Variability Methods Input Output

This server calculates the sequence variability within a multiple sequence alignment using several variability metrics. Subsequently, the server can perform several tasks, such as masking the variability in the reference sequence, returning conserved fragments or mapping the sequence variability onto a provided 3D-structure.

INPUT
Choose your input data type:
Protein Alignment
( Valid formats are: CLUSTAL, FASTA, GCC/PILEUP)
PDB File
Paste your alignment.
or Upload Alignment
Get PDB file from PDB code   
or Upload your PDB File    
Chain ID   

SEQUENCE VARIABILITY OPTIONS
Select Variability Method
Shannon Simpson Wu-Kabat
Select Reference Sequence:
 Consensus sequence  First sequence in alignment

OUTPUT TASKS
Plot variability
Plot variability
Map structural variability
    PDB file:
Plot variability
Map structural variability
Map structural variability
    PDB file:
Map structural variability
Mask sequence variability
Return conserved fragment of length  
      Enter Variability threshold:  

    

Citation:
  • Diez-Rivero CM & Reche PA. (2009). Discovery of conserved epitopes through sequence variability analysis. Bioinformatics for immunomics; Series: Immunomics Reviews: Vol. 3. Pg. 95-101. Eds. Flower, Darren D.R.; Davies, Matthew; Ranganathan, Shoba. ISBN: 978-1-4419-0539-0.
     
  • Garcia-Boronat M, Diez-Rivero CM, Reinherz EL, Reche PA (2008) PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Res., 36:W35-41.
     
Praises and Complaints: Pedro A. Reche
 
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