Table 1.

Bioinformatics tools, web servers and tutorials relevant as part of the vaccine target discovery pipeline described herein

Tool	URL (http or ftp)
AVANA	http://sourceforge.net/projects/avana/
BioEdit	http://www.mbio.ncsu.edu/bioedit/bioedit.html
BLAST Web server	http://blast.ncbi.nlm.nih.gov/
BLAST+	http://tinyurl.com/259v9pq
BLAST+ Databases	ftp://ftp.ncbi.nlm.nih.gov/blast/db/
BLAST+ Manual	http://tinyurl.com/njr9xk6
BLAST2GO	https://www.blast2go.com/
CDD	http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
ClustalX	ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
HCV Immunology Database	https://hcv.lanl.gov/content/immuno/immuno-main.html
HIV Molecular Immunology Database	https://www.hiv.lanl.gov/content/immunology/
HIV Sequence Database	https://www.hiv.lanl.gov/
Immune Epitope Database	http://www.iedb.org/
Influenza Database	http://research4.dfci.harvard.edu/cvc/flukb/
Jalview	http://www.jalview.org
MHCBN	http://crdd.osdd.net/raghava/mhcbn/
MULTIPRED2	http://cvc.dfci.harvard.edu/multipred2/
Muscle	http://www.drive5.com/muscle/
NCBI Entrez Databases	http://www.ncbi.nlm.nih.gov
NCBI Entrez Protein Database	http://www.ncbi.nlm.nih.gov/protein
NCBI Entrez Taxonomy Database	http://www.ncbi.nlm.nih.gov/taxonomy
NetCTL	http://www.cbs.dtu.dk/services/NetCTL
PEPVAC	http://imed.med.ucm.es/PEPVAC/
Pfam	http://pfam.xfam.org/
PROMALS3D	http://prodata.swmed.edu/promals3d/promals3d.php
Prosite	http://www.expasy.org/prosite
R	http://www.r-project.org
SYFPEITHI	http://www.syfpeithi.de
Tutorial 1: create BLAST searchable database	http://tinyurl.com/4bl2qlv
Tutorial 2: remove duplicate sequences	http://tinyurl.com/yadxuqe
Tutorial 3: generate tabbed alignment file (in.taln format) for input to AVANA	http://tinyurl.com/6cjb4gg
Tutorial 4: Notes on performing BLAST search with short queries	http://tinyurl.com/4uw5nd9
UniProt	http://www.uniprot.org