| Title: |
VIRULIGN: fast codon-correct alignment and annotation of viral genomes |
| Authors: |
Libin, Pieter J.K.; Deforche, Koen; Abecasis, Ana B.; Theys, Kristof |
| Source: |
ISSN:1367-4803 ; ISSN:1460-2059 ; Bioinformatics, vol. 35 (10), (1763-1765. |
| Publisher Information: |
Oxford University Press |
| Publication Year: |
2019 |
| Subject Terms: |
Science & Technology; Life Sciences & Biomedicine; Technology; Physical Sciences; Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer Science; Interdisciplinary Applications; Mathematical & Computational Biology; Statistics & Probability; Biochemistry & Molecular Biology; Mathematics; MULTIPLE SEQUENCE ALIGNMENT; DYNAMICS; Codon; Genome; Viral; Software; 01 Mathematical Sciences; 06 Biological Sciences; 08 Information and Computing Sciences; Bioinformatics; 31 Biological sciences; 46 Information and computing sciences; 49 Mathematical sciences |
| Description: |
SUMMARY: Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit of these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codon-correct alignments of large datasets, with standardized and formalized genome annotation and various alignment export formats. AVAILABILITY AND IMPLEMENTATION: VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project. SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online. ; sponsorship: Pieter Libin is funded by a doctoral grant of the Research Foundation - Flanders (FWO). This work has been partially funded by the Fundacao para a Ciencia e Tecnologia (FCT) through funds to GHTM-UID/Multi/04413/2013 and by the MigrantHIV project (PTDC/DTP-EPI/7066/2014). We thank A.-M. Vandamme, S. Imbrechts, L. Cuypers and F. Ferreira for testing the software. We thank the three anonymous reviewers for their comments, as they have helped us to improve the software and manuscript. (Research Foundation - Flanders (FWO), Fundacao para a Ciencia e Tecnologia (FCT)|GHTM-UID/Multi/04413/2013, MigrantHIV project|PTDC/DTP-EPI/7066/2014) ; status: Published |
| Document Type: |
article in journal/newspaper |
| File Description: |
application/pdf |
| Language: |
English |
| Relation: |
https://lirias.kuleuven.be/handle/123456789/628594; https://doi.org/10.1093/bioinformatics/bty851; https://pubmed.ncbi.nlm.nih.gov/30295730 |
| DOI: |
10.1093/bioinformatics/bty851 |
| Availability: |
https://lirias.kuleuven.be/handle/123456789/628594; https://lirias.kuleuven.be/retrieve/73cd59c7-9e83-4a35-88e8-b33092a741f5; https://doi.org/10.1093/bioinformatics/bty851; https://pubmed.ncbi.nlm.nih.gov/30295730 |
| Rights: |
info:eu-repo/semantics/openAccess ; public |
| Accession Number: |
edsbas.AFB6258 |
| Database: |
BASE |