Tsimpidis Michail, Bachoumis Georgios, Mimouli Kalliopi, Kyriakopoulou Zaharoula, Robertson David L, Markoulatos Panayotis, Amoutzias Grigoris D
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.
BMC Bioinformatics. 2017 Jan 5;18(1):13. doi: 10.1186/s12859-016-1420-z.
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.
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.
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.
许多用于检测病毒重组的计算工具并不适用于当前的基因组革命。需要一种计算工具，它能够快速扫描数百/数千个基因组或序列片段，并检测出候选重组事件，这些事件随后可通过更敏感和专门的方法进行进一步分析。
T-RECs是一个基于Windows的图形工具，它采用滑动窗口的成对比对，并且能够执行（i）基因分型，（ii）新基因组的聚类，（iii）检测不同进化谱系之间最近的重组事件，（iv）通过相似性图对检测到的重组事件进行人工检查，以及（v）基因组区域的注释。
对555个诺如病毒全基因组和2500个序列片段的分析表明，T-RECs非常有效，在该分析中，在ORF1-ORF2连接处鉴定出一个重组热点。
