Publication
ViruScopeDB: a comprehensive multi-omics database for highly infectious viruses
| dc.contributor.author | Lima, Ana | |
| dc.contributor.author | Carneiro, João | |
| dc.contributor.author | Sousa, Sérgio | |
| dc.contributor.author | Sá, Vítor | |
| dc.contributor.author | Pratas, Diogo | |
| dc.contributor.author | Sá, Vítor J. | |
| dc.date.accessioned | 2025-11-12T14:55:19Z | |
| dc.date.available | 2025-11-12T14:55:19Z | |
| dc.date.issued | 2025-05 | |
| dc.description.abstract | Highly infectious viruses such as HIV, Ebola, and SARS-CoV-2 have presented ongoing challenges to global health. Consequently, the optimization of rapid detection tests, including PCR, and the identification of new therapeutic targets remain of paramount importance. The development of genomic and proteomic databases like the HIV Oligonucleotide Database (HIVoligoDB) [1], EbolaID [2], and CoV2ID [3] has facilitated the accumulation and accessibility of knowledge through comprehensive, user-friendly, open-access platforms. This study aims to update, expand, and integrate these databases into a single resource, ViruScopeDB, while conducting thorough analyses of informative genomic regions with the goal of enhancing viral detection methods and treatment strategies. Complete genomic sequence variants for each virus were compiled using NCBI Virus, followed by multiple sequence alignment via MAFFT within the Galaxy platform. The alignments were consequently uploaded to Geneious Prime for complete genome visualization and calculation of parameters such as percentage of pairwise identity. Primer data was extracted from open-access research articles available on PubMed using a newly-built custom pipeline for PDF to plain text conversion followed by data mining of oligonucleotide sequences. A fully automated script for primer validation, parameter scoring and calculation of best primer pairs for PCR is being constructed for subsequent upload into the database. A total of 658 sequences with a mean length of 18,910 base pairs (bp) were collected for Ebolavirus, with percentage of pairwise identity (PPI) of 91.7%. 7,261 sequences with a mean length of 8,883 bp, with a PPI of 80.8% were identified for HIV-1. For HIV-2, 43 sequences with an average of 10,108 bp and PPI of 80.9% were analyzed. For Ebola, a total of 709 primers were scraped from 257 articles, and for HIV articles this number rises to 10,290 primers collected from 2,579 articles. Using a combination of preexistent and novel custom-built bioinformatics tools, it was possible to data mine key information related to each virus and their variants, as well as collect primer information for possible PCR optimizations. Further analysis will be conducted on the data collected, branching out into the realm of phylogenetics and 3D modelling/viral protein docking, in order to construct a database that is transversal to various omics. | por |
| dc.identifier.citation | Lima, A., Carneiro, J., Sousa, S., Sá, V., & Pratas, D. (2025). ViruScopeDB: a comprehensive multi-omics database for highly infectious viruses. Livro de Resumos do 18º Encontro de Investigação Jovem da U.Porto, 1032–1033. https://www.up.pt/ijup/wp-content/uploads/sites/892/2025/06/Livro-de-Resumos_IJUP-2025.pdf | |
| dc.identifier.isbn | 978-989-746-418-8 | |
| dc.identifier.uri | http://hdl.handle.net/10400.22/30856 | |
| dc.language.iso | eng | |
| dc.peerreviewed | yes | |
| dc.publisher | Universidade do Porto | |
| dc.relation | UIDB/04423/2020 (CIIMAR) and UIDP/04423/2020 (CIIMAR) 10.54499/LA/P/0008/2020,10.54499/UIDP/50006/2020, UIDB/04050/2020 (UMinho CBMA); 10.54499/UIDB/50006/2020 (LAVQ), UIDB/00319/2020 (ALGORITMI/LASI) and UIDB/00127/2020 (IEETA/LASI - doi.org/10.54499/UIDB/00127/2020) | |
| dc.relation.hasversion | https://www.up.pt/ijup/wp-content/uploads/sites/892/2025/06/Livro-de-Resumos_IJUP-2025.pdf | |
| dc.rights.uri | N/A | |
| dc.subject | Bioinformatics | |
| dc.subject | Virology | |
| dc.subject | Database | |
| dc.subject | Ddata mining | |
| dc.title | ViruScopeDB: a comprehensive multi-omics database for highly infectious viruses | por |
| dc.type | conference poster | |
| dspace.entity.type | Publication | |
| oaire.citation.conferenceDate | 2025-05 | |
| oaire.citation.conferencePlace | Porto | |
| oaire.citation.endPage | 1033 | |
| oaire.citation.startPage | 1032 | |
| oaire.citation.title | Livro de Resumos do 18º Encontro de Investigação Jovem da U.Porto | |
| oaire.version | http://purl.org/coar/version/c_970fb48d4fbd8a85 | |
| person.familyName | Sá | |
| person.givenName | Vítor J. | |
| person.identifier | C-8775-2009 | |
| person.identifier.ciencia-id | 211C-CF41-90E7 | |
| person.identifier.orcid | 0000-0002-4982-4444 | |
| person.identifier.rid | C-8775-2009 | |
| person.identifier.scopus-author-id | 49864475600 | |
| relation.isAuthorOfPublication | 89f27ca4-b34c-4813-9c23-2d7300d1743d | |
| relation.isAuthorOfPublication.latestForDiscovery | 89f27ca4-b34c-4813-9c23-2d7300d1743d |