Table 1.
Web servers related to PVS
| Web server | Input: formats | Output and tasks | Ref |
|---|---|---|---|
| • PVS http://imed.med.ucm.es/PVS/ | • MSA: CLUSTAL, FASTA, GCG/MSF • PDB: Uploaded or retrieved • MSA and PDB |
1. Compute sequence variability 2. Plot sequence variability 3. Map and display variability in 3D structures 4. Mask sequence variability 5. T-cell epitope prediction 6. Return conserved fragments 7. Locate conserved fragments into 3D structures/B-cell epitope prediction |
|
| • SVS* http://bio.dfci.harvard.edu/Tools/svs.html | • MSA: CLUSTAL | 1. Compute sequence variability as given by Shannon Entropy 2. Plot sequence variability 3. Return conserved fragments |
|
| • SiteVarProt http://159.149.109.16/Tools/SiteVarProt.php | • MSA: FASTA | 1. Compute relative sequence variability 2. Plot sequence variability |
(35) |
| • Consensus http://coot.embl.de/Alignment//consensus.html | • MSA: CLUSTAL and GCG/MSF | 1. Consensus sequence at various thresholds with amino acid groupings | |
| • Conseq http://conseq.bioinfo.tau.ac.il/ | • SEQUENCE: FASTA • MSA: NBRF/PIR, EMB, FASTA, GDE, CLUSTAL, GCG/MSF and RSF |
1. Compute conservation scores 2. Compute solvent accessibility 3. Return color-coded sequence with calculations |
(9) |
| • Consurf http://consurf.tau.ac.il/ | • PDB: Uploaded or retrieved • MSA and PDB |
1. Compute conservation scores 2. Map and display conservation scores in 3D structures |
(11) |
| • TreeDet http://www.pdg.cnb.uam.es/Servers/treedet/ | • MSA: CLUSTAL, FASTA, MSF and PIR | • Predicts and display functionally relevant residues | (10) |
| • Conservancy http://tools.immuneepitope.org/tools/conservancy | • SEQUENCES: FASTA | • Computes per site sequence identity of epitopes in protein sources | (36) |
PVS is an enhanced version of SVS, a server previously developed by Dr Reche. SVS has >85 000 hits since it started running in 2002.