EbolaID DATABASE PROJECT

EbolaID provides a complete, quality checked and regularly updated list of oligonucleotides for the Ebola virus. The database describes the genetic diversity across the Ebola genome to facilitate the design of accurate diagnostic methods and therapeutic approaches.


What can be done in EbolaID

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

Reference genome>> Obtain the reference Ebola genome sequence

Sequence alignments>> Explore the genetic diversity across Ebola genomes

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

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

Ebola virus particles




Database content

Total number of oligonucleotides: 80 Number of PCR primers: 69 Number of probes: 11 Number of publications: 27
Localization of oligonucleotides (green arrows) in the Ebola virus reference genome

What can be found in EbolaID


Search for the best oligonucleotides according
to the degree of conservation
in specific sequence alignments
Select the most conserved/variable regions
across the Ebola 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
Find information on the sequence conservation
measures used in this site
Conserved
genomic regions
Select the best alignment according to
different measure of sequence conservation
PCR primer pairs
The best oligonucleotides
Our sequence
conservation measures
The top alignments
Oligonucleotides
in specific alignments


The best oligonucleotides

Top oligonucleotides
Oligonucleotide EbolaID score
EBOLAID051 87.51
EBOLAID039 87.24
EBOLAID027 86.75
EBOLAID036 86.10
EBOLAID037 86.10
Top PCR primer pairs
Primer 1 Primer 2 EbolaID score
EBOLAID039 EBOLAID051 87.54
EBOLAID028 EBOLAID051 87.53
EBOLAID028 EBOLAID036 86.83
EBOLAID028 EBOLAID037 86.83
EBOLAID028 EBOLAID038 86.83



News

1/3/2017 - Database updated with 23 new oligonucleotides from 10 peer-reviewed publications.

6/3/2017 - New multiple sequence alignment with all available full Ebola virus genomes (n=1610) from the 2013-2016 outbreak.

Contacts

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

Reference

"EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment"
João Carneiro and Filipe Pereira 2016 PLOS Negl Trop Dis 10 (7), e0004757