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Protocols

BioAfrica specifications

Information


Unique identifier OMICS_20921
Name BioAfrica
Alternative name BioAfrica HIV-1 Proteomics Resource
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Maintainers


  • person_outline Tulio De Oliveira
  • person_outline Tulio De Oliveira

Publication for BioAfrica

BioAfrica citations

 (38)
library_books

Co circulation and simultaneous co infection of dengue, chikungunya, and zika viruses in patients with febrile syndrome at the Colombian Venezuelan border

2018
BMC Infect Dis
PMCID: 5791178
PMID: 29382300
DOI: 10.1186/s12879-018-2976-1

[…] s obtained were compared with various prototype strains of each of these viruses using BLAST and the on-line tool, Dengue, Zika & Chikungunya Viruses Typing Tool Version 0.9 – Alpha (available at www.bioafrica.net/software.php). […]

library_books

Genomic and epidemiological characterisation of a dengue virus outbreak among blood donors in Brazil

2017
Sci Rep
PMCID: 5680240
PMID: 29123142
DOI: 10.1038/s41598-017-15152-8

[…] s were removed from subsequent analysis to avoid introducing biases in evolutionary rate estimates. DENV types were classified using the Dengue, Zika and Chikungunya Viruses Typing Tool v.0.9 (http://bioafrica2.mrc.ac.za/rega-genotype-alpha/aedesviruses/typingtool/). […]

call_split

Characterization of Nucleoside Reverse Transcriptase Inhibitor Associated Mutations in the RNase H Region of HIV 1 Subtype C Infected Individuals

2017
Viruses
PMCID: 5707537
PMID: 29117130
DOI: 10.3390/v9110330
call_split See protocol

[…] nsed software programs (http://www.phrap.org/phredphrapconsed.html) and aligned against HXB2 reference strain []. The alignment was manually edited using the Genetic Data Environment v2.2 (http://www.bioafrica.net/GDElinux/GDEmicrobial). HIV-1 subtype was determined by the REGA HIV-1 subtyping tool version 3 [,]. A maximum likelihood phylogenetic tree was built with PhyML using the GTR substitutio […]

library_books

Expanding HIV 1 subtype B transmission networks among men who have sex with men in Poland

2017
PLoS One
PMCID: 5325290
PMID: 28234955
DOI: 10.1371/journal.pone.0172473

[…] om the start of HXB2 genome: positions 2253 to 3525. Identification of subtype B was performed based on the partial pol sequences using two methods: on-line software (REGA genotyping 2.0 tool; http://bioafrica.mrc.ac.za/rega-genotype/html/subtypinghiv.html) and phylogenetic analyses using maximum likelihood (ML) method under the GTR+γ model with approximate likelihood ratio test (aLRT) (online PHY […]

library_books

Spatiotemporal dynamics of HIV 1 transmission in France (1999–2014) and impact of targeted prevention strategies

2017
Retrovirology
PMCID: 5322782
PMID: 28222757
DOI: 10.1186/s12977-017-0339-4

[…] HIV-1 subtypes were determined uploading sequences individually into the REGA HIV-1 automated Subtyping Tool version 2.0 (http://www.bioafrica.net/rega-genotype/html/subtypinghiv.html) and confirmed by in-house phylogenetic analysis.The age of the most recent common ancestor (TMRCA, years) and the ancestral geographic movements wer […]

call_split

The PTAP sequence duplication in HIV 1 subtype C Gag p6 in drug naive subjects of India and South Africa

2017
BMC Infect Dis
PMCID: 5259826
PMID: 28118816
DOI: 10.1186/s12879-017-2184-4
call_split See protocol

[…] contained a total of 1,632 nucleic acid positions. Additionally, genetic subtype characterization of the gag sequences was performed using the REGA HIV-1 Subtyping Tool version 2.0, available at the BioAfrica site (http://www.bioafrica.net/rega-genotype/html/) and the recombinant identification tool available at the Los Alamos HIV Sequence Database (http://hiv.lanl.gov/content/index). Every indiv […]

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BioAfrica institution(s)
Africa Centre for Population Health, School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Division of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa; Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
BioAfrica funding source(s)
Supported by the Swiss South African Joint Research Programme (SSJRP) research grant entitled "Swiss Prot / South Africa: Protein Bioinformatics Resource Development for Important Health- related Pathogens, the Swiss Federal Government through the State Secretariat for Education, Research and Innovation, Flagship grant from the Medical Research Council (MRC) of the Republic of South Africa (MRCRFA-UFSP-01-2013/UKZN HIVEPI) the Wellcome Trust (082384/Z/07/Z) and a Royal Society Newton Advanced Fellowship.

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