HIVoligoDB - The HIV oligonucleotide database

The HIVoligoDB is a comprehensive on-line resource with curated datasets of oligonucleotides for the human immunodeficiency virus (HIV). The database provides a curated and regularly updated list of oligonucleotides and a description of the genetic diversity across the HIV-1 and HIV-2 genomes to facilitate the design of accurate diagnostic methods and therapeutic approaches.


Last update: January 2017 (Oligonucleotides melting temperature and free energy added)

What can be done in HIVoligoDB

HIV virus
HIV>> Find a brief description of the HIV

Reference genome>> Obtain the reference HIV genome sequence

Sequence alignments>> Explore the genetic diversity across HIV genomes

Oligonucleotides>> Find the best targets for your HIV identification system

Search>> Find several tables with different measures of sequence conservation

HIV




Database content

Total number of oligonucleotides:
HIV-1: 380
HIV-2:65
Number of PCR primers:
HIV-1: 237
HIV-2: 57
Number of probes:
HIV-1: 143
HIV-2: 8
Number of publications: 54
Localization of oligonucleotides (green arrows) in the HIV-1 reference genome

What can be found in HIVoligoDB


HIV-2
HIV-1
Select the most conserved/variable regions
across the HIV-1 genome
Find PCR primer pairs ordered by the average
degree of conservation
in diverse sequence alignments
Search for oligonucleotides described
in peer reviewed publications ordered
by the average degree of conservation
in diverse sequence alignments
Conserved
genomic regions
PCR primer pairs
The best oligonucleotides
Select the most conserved/variable regions
across the HIV-2 genome
Find PCR primer pairs ordered by the average
degree of conservation
in diverse sequence alignments
Search for oligonucleotides described
in peer reviewed publications ordered
by the average degree of conservation
in diverse sequence alignments
Conserved
genomic regions
PCR primer pairs
The best oligonucleotides


The best oligonucleotides HIV-1

Top oligonucleotides
Oligonucleotide Score
HIV1ID0037 81.79
HIV1ID0146 79.43
HIV1ID0179 78.91
HIV1ID0163 78.87
HIV1ID0116 78.38
Top PCR primer pairs
Primer 1 Primer 2 Score
HIV1ID0037 HIV1ID0179 80.35
HIV1ID0037 HIV1ID0163 80.33
HIV1ID0037 HIV1ID0073 78.75
HIV1ID0179 HIV1ID0182 78.40
HIV1ID0163 HIV1ID0182 78.39

The best oligonucleotides HIV-2

Top oligonucleotides
Oligonucleotide Score
HIV2ID0015 95.13
HIV2ID0061 87.48
HIV2ID0057 84.70
HIV2ID0044 83.47
HIV2ID0017 82.91
Top PCR primer pairs
Primer 1 Primer 2 Score
HIV2ID0015 HIV1ID0061 91.31
HIV2ID0057 HIV2ID0061 86.10
HIV2ID0024 HIV2ID0061 83.30
HIV2ID0041 HIV2ID0044 82.39
HIV1ID0012 HIV1ID0015 82.30



Contacts


Filipe Pereira - fpereirapt@gmail.com
João Carneiro - joaomiguelsov@gmail.com
CIIMAR UPorto
FCT