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

Tsimpidis, M., Bachoumis, G., Mimouli, K., Kyriakopoulou, Z., Robertson, D. L. , Markoulatos, P. and Amoutzias, G. D. (2017) T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. BMC Bioinformatics, 18, 13. (doi: 10.1186/s12859-016-1420-z) (PMID:28056784) (PMCID:PMC5216575)

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.

• Item Type: Articles
• Additional Information: This work has been supported and implemented under the "ARISTEIA II" Action of the "OPERATIONAL PROGRAMME EDUCATION AND LIFELONG LEARNING" and is co-funded by the European Social Fund (ESF) and National Resources (code 4288 to G.D.A) and also supported by the research grants from the Postgraduate Programme ‘Applications of Molecular Biology-Genetics, Diagnostic Biomarkers’, code 3817 of the University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Robertson, Professor David
• Authors: Tsimpidis, M., Bachoumis, G., Mimouli, K., Kyriakopoulou, Z., Robertson, D. L., Markoulatos, P., and Amoutzias, G. D.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: BMC Bioinformatics
• Publisher: Biomed Central
• ISSN: 1471-2105
• ISSN (Online): 1471-2105
• Copyright Holders: Copyright © 2017 The Authors
• First Published: First published in BMC Bioinformatics 18: 13
• Publisher Policy: Reproduced under a Creative Commons License