Bioinformatics in New Generation Flavivirus Vaccines

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