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Vacceed specifications

Information


Unique identifier OMICS_19933
Name Vacceed
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Thousands of protein sequences from the target pathogen.
Output data A ranked vaccine candidate list of all proteins in the target pathogen based on an average probability of individual classifier predictions.
Operating system Unix/Linux
Programming languages Perl, Shell (Bash)
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline John Ellis
  • person_outline Paul Kennedy

Publication for Vacceed

Vacceed citations

 (5)
library_books

Vaccines Meet Big Data: State of the Art and Future Prospects. From the Classical 3Is (“Isolate–Inactivate–Inject”) Vaccinology 1.0 to Vaccinology 3.0, Vaccinomics, and Beyond: A Historical Overview

2018
PMCID: 5845111
PMID: 29556492
DOI: 10.3389/fpubh.2018.00062

[…] to aid and assist researchers in vaccine discovery and design (, ). Databases of vaccine candidates, such as MalVac (), or Vaxar (), software tools such as Vaxjo (), VIOLIN (–), NERVE (), Vaxign (), Vacceed (), Jenner-predict server (), EpiToolKit (), iVax (), or VaxiJen (), have been specifically implemented for vaccinology to enable prediction of vaccine antigens or adjuvants.A successful examp […]

library_books

The genome of the protozoan parasite Cystoisospora suis and a reverse vaccinology approach to identify vaccine candidates☆

2017
PMCID: 5354109
PMID: 28161402
DOI: 10.1016/j.ijpara.2016.11.007

[…] Initially, 403 protein sequences containing unknown amino acids (‘X’) were filtered out. The software Vacceed () was used to identify potential immunogenic proteins. Vacceed implements a machine learning approach that combines independent sources of evidence for immunogenic features computed by differ […]

library_books

Cloning, expression and molecular characterization of a Cystoisospora suis specific uncharacterized merozoite protein

2017
PMCID: 5297187
PMID: 28173829
DOI: 10.1186/s13071-017-2003-1

[…] te a rich reservoir for species-specific antigens and thus putative targets for immune-intervention. In line with this trend, previous screening of the predicted proteome of C. suis with the software Vacceed revealed numerous potential vaccine candidates with no annotated function []. Among these, CSUI_005805, which encodes for an uncharacterized protein, appeared to be an attractive candidate owi […]

library_books

Vaccination against parasites – status quo and the way forward

2016
PMCID: 5382507
PMID: 28405456
DOI: 10.1186/s40813-016-0047-9

[…] s (Palmieri, submitted). For C. suis a genome size of 83 Megabases encoding >8300 genes is estimated, and a recently developed pipeline for the search of vaccine candidates in apicomplexan parasites (Vacceed; []) has detected 562 candidates in C. suis which now need to be evaluated further in silico, in vitro (using a cell culture system supporting the complete life cycle of C. suis; []) and in vi […]

library_books

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens

2015
J Immunol Res
PMCID: 4615220
PMID: 26526043
DOI: 10.1155/2015/156241

[…] HC I and MHC II epitope prediction. Jenner-Predict, while using some of the same filtering criteria as NERVE and Vaxign, put more weight on the known host-pathogen interaction domains on proteins []. Vacceed framework extended the vaccine antigen prediction also to eukaryotes [], which are typically much more challenging targets due to their complexity compared to prokaryotes. Also approaches base […]

Citations

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Vacceed institution(s)
School of Medical and Molecular Biosciences, The ithree Institute, University of Technology Sydney (UTS), Ultimo, NSW, Australia; Faculty of Engineering and Information Technology, School of Software, The Centre for Quantum Computation and Intelligent Systems, University of Technology Sydney (UTS), Ultimo, NSW, Australia
Vacceed funding source(s)
Supported by PhD scholarship from Zoetis (Pfizer) Animal Health.

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