T-RECs: Rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes

Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos, Grigoris D. Amoutzias

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number13
JournalBMC Bioinformatics
Volume18
Issue number1
DOIs
Publication statusPublished - 5 Jan 2017

Keywords

  • Graphical tool
  • Norovirus
  • Pairwise alignment
  • Recombination
  • Similarity plot
  • Virus

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