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T-RECs: Rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes
dc.creator | Tsimpidis M., Bachoumis G., Mimouli K., Kyriakopoulou Z., Robertson D.L., Markoulatos P., Amoutzias G.D. | en |
dc.date.accessioned | 2023-01-31T10:14:31Z | |
dc.date.available | 2023-01-31T10:14:31Z | |
dc.date.issued | 2017 | |
dc.identifier | 10.1186/s12859-016-1420-z | |
dc.identifier.issn | 14712105 | |
dc.identifier.uri | http://hdl.handle.net/11615/79976 | |
dc.description.abstract | Background: Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods. Results: T-RECs, a Windows based graphical tool, employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions. Conclusions: T-RECs is very effective, as demonstrated by an analysis of 555 Norovirus complete genomes and 2500 sequence fragments, where a recombination hotspot was identified at the ORF1-ORF2 junction. © 2017 The Author(s). | en |
dc.language.iso | en | en |
dc.source | BMC Bioinformatics | en |
dc.source.uri | https://www.scopus.com/inward/record.uri?eid=2-s2.0-85008164769&doi=10.1186%2fs12859-016-1420-z&partnerID=40&md5=7fc39e2336de8f3c62eb2a9fc9d89a68 | |
dc.subject | Computational methods | en |
dc.subject | Viruses | en |
dc.subject | Graphical tools | en |
dc.subject | Norovirus | en |
dc.subject | Pairwise alignment | en |
dc.subject | Recombination | en |
dc.subject | Similarity plot | en |
dc.subject | Genes | en |
dc.subject | genotype | en |
dc.subject | nonhuman | en |
dc.subject | Norovirus | en |
dc.subject | virus genome | en |
dc.subject | cluster analysis | en |
dc.subject | DNA fragmentation | en |
dc.subject | DNA sequence | en |
dc.subject | genetic database | en |
dc.subject | genetic recombination | en |
dc.subject | genetics | en |
dc.subject | genotyping technique | en |
dc.subject | molecular evolution | en |
dc.subject | Norovirus | en |
dc.subject | sequence alignment | en |
dc.subject | software | en |
dc.subject | virus DNA | en |
dc.subject | Cluster Analysis | en |
dc.subject | Databases, Genetic | en |
dc.subject | DNA Fragmentation | en |
dc.subject | DNA, Viral | en |
dc.subject | Evolution, Molecular | en |
dc.subject | Genome, Viral | en |
dc.subject | Genotyping Techniques | en |
dc.subject | Norovirus | en |
dc.subject | Recombination, Genetic | en |
dc.subject | Sequence Alignment | en |
dc.subject | Sequence Analysis, DNA | en |
dc.subject | Software | en |
dc.subject | BioMed Central Ltd. | en |
dc.title | T-RECs: Rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes | en |
dc.type | journalArticle | en |
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