Benavente Ernest D, Coll Francesc, Furnham Nick, McNerney Ruth, Glynn Judith R, Campino Susana, Pain Arnab, Mohareb Fady R, Clark Taane G
Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St, London, UK.
Engineering Sciences Division, School of Engineering, Cranfield University, Cranfield, UK.
BMC Bioinformatics. 2015 May 13;16(1):155. doi: 10.1186/s12859-015-0603-3.
Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria. One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting.
We have developed a web-based tool called PhyTB ( http://pathogenseq.lshtm.ac.uk/phytblive/index.php ) to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant Call Format files can be uploaded to determine a sample position within the tree. A map view summarises the geographical distribution of alleles and strain-types. The utility of the PhyTB is demonstrated on sequence data from 1,601 M. tuberculosis isolates.
PhyTB contextualises M. tuberculosis genomic variation within epidemiological, geographical and phylogenic settings. Further tool utility is possible by incorporating large variants and phenotypic data (e.g. drug-resistance profiles), and an assessment of genotype-phenotype associations. Source code is available to develop similar websites for other organisms ( http://sourceforge.net/projects/phylotrack ).
基于系统发育的结核分枝杆菌及其他细菌基因组分类是研究进化假说、疾病暴发和传播事件的核心分析方法。全基因组测序为深入了解菌株内和菌株间多样性背后的基因组变异提供了新的视角，从而有助于细菌的分类和分子条形码分析。菌株研究的一个障碍是缺乏用户交互式解决方案来在系统发育树环境中查询和可视化变异。
PhyTB在流行病学、地理和系统发育背景下将结核分枝杆菌基因组变异情境化。通过纳入大变异和表型数据（如耐药谱）以及评估基因型-表型关联，该工具可能具有更大的实用性。源代码可用于为其他生物体开发类似网站（http://sourceforge.net/projects/phylotrack）。
