Table 2.
Selection of servers and programs that could assist in the rational design of vaccines.
| Server | Web address | Server description | Availability |
|---|---|---|---|
| ORF-FINDER | http://www.ncbi.nlm.nih.gov/projects/gorf/ | Program identifies open reading frames in a genome. | Free online |
| GeneMark | http://exon.biology.gatech.edu/ | A set of gene prediction servers for prokaryotes, eukaryotes and viruses | Free online |
| NERVE | http://www.bio.unipd.it/molbinfo/ | In silico prediction of vaccine candidates from complete proteomes of bacterial pathogens | Free for download |
| Gene Composer | http://www.genecomposer.net/ | Gene Composer is a software program for rational design or optimization of genes | Free demo for 1 year |
| PromoterScan | http://www-bimas.cit.nih.gov/molbio/proscan/ | Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences | Free online |
| ATGpr | http://flj.hinv.jp/ATGpr/atgpr/index.html | A program for identifying the initiation codons in cDNA sequences | Free online |
| PolyApred | http://www.imtech.res.in/raghava/polyapred/ | PolyApred is a SVM based method for the prediction of polyadenylation signal in human DNA sequence. | Free online |
| NetGene2 | http://genome.cbs.dtu.dk/services/NetGene2/ | Predictions of splice sites in human | Free online |
| SignalP | http://www.cbs.dtu.dk/services/SignalP/ | Signal peptide and cleavage sites in prokaryotic and eukaryotic sequences | Free online |
| Optimizer | http://genomes.urv.es/OPTIMIZER/ | A web server for optimization of codon usage of a DNA sequence to increase its expression level. | Free online |
| CodonExplorer | http://bmf2.colorado.edu/codonexplorer/index.psp | Online tool for analyzing GC content and codon usage frequency | Free online, registration required |
| STAR | http://biology.leidenuniv.nl/~batenburg/STROrder.html | STAR simulates the folding pathway of RNA and is able to predict formation of pseudoknots formation | Commercially available |
| VIENNA package | http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi | RNAfold predicts secondary structure of single stranded RNA or DNA based on minimum free energy predictions | Commercially available |
| mFOLD | http://mfold.bioinfo.rpi.edu/ | Prediction of RNA and DNA secondary structure based on thermodynamic methods | Free online |
| DyNAVacS | http://miracle.igib.res.in/dynavac/ | An integrative tool for optimized DNA vaccine design | Free onliune |
| AlgPred | http://www.imtech.res.in/raghava/algpred/ | Algpred allows prediction of allergens based on similarity of known epitope with any region of protein | Free online |
| BIMAS | http://www-bimas.cit.nih.gov/molbio/hla_bind/ | Server for prediction of MHC-I epitopes | Free online |
| EpiPredict | http://www.imtech.res.in/raghava/mhc2pred/ | Software to predict HLA-class II restricted T cell epitopes and ligands | Free online |
| SYFPEITHI | http://www.syfpeithi.de/ | Server for prediction of MHC-I and MHC-II epitopes | Free online |
| RANKPEP | http://bio.dfci.harvard.edu/RANKPEP/ | Server for prediction of MHC-I and MHC-II epitopes | Free online |
| CEP | http://202.41.70.74:8080/cgi-bin/cep.pl | Server for prediction conformational B cell epitopes | Free online |
| Bcipep | http://www.imtech.res.in/raghava/bcipep/pep_src.html | Bcipep is a database with a collection of immunogenic B cell peptides | Free online |
| ABCpred | http://www.imtech.res.in/raghava/abcpred/ | Server for prediction conformational B cell epitopes | Free online |
| ePitope | http://www.epitope-informatics.com/ | Server for prediction linear B cell epitopes | Online, commercial |
| TollML | http://tollml.lrz.de/ | A user-friendly database to retrieve sequence and structural data as well as ligands for TLRs. | Free online |
| Virology Bioinformatics | http://www.bioinfo.de/isb/2008/08/0008/ | A collection of bioinformatic tools for virology research | Free online |
| VBRC | http://athena.bioc.uvic.ca/ | VBRC provides access to viral genomes and a variety of bioinformatic tools for comparative genomic analyses | Free online |