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

BMC Bioinformatics

Software

Georgios Bachoumis¹  Grigoris D. Amoutzias¹  Michail Tsimpidis¹  Kalliopi Mimouli¹  Panayotis Markoulatos²  Zaharoula Kyriakopoulou²  David L. Robertson³ 

[1] Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece;Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece;Faculty of Life Sciences, University of Manchester, Manchester, UK;

关键词: Virus;    Recombination;    Pairwise alignment;    Similarity plot;    Graphical tool;    Norovirus;   

DOI  :  10.1186/s12859-016-1420-z

 received in 2016-08-30, accepted in 2016-12-10,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundMany 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.ResultsT-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.ConclusionsT-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.

【 授权许可】

CC BY   
© The Author(s). 2017