Table 1 Bioinformatics tools, web servers and tutorials relevant as part of the vaccine target discovery pipeline described herein

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