Faculties of Epidemiology & Population Health and Infectious & Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.
Bioinformatics. 2012 Nov 15;28(22):2983-5. doi: 10.1093/bioinformatics/bts557. Epub 2012 Sep 13.
There is an immediate need for tools to both analyse and visualize in real-time single-nucleotide polymorphisms, insertions and deletions, and other structural variants from new sequence file formats. We have developed VarB software that can be used to visualize variant call format files in real time, as well as identify regions under balancing selection and informative markers to differentiate user-defined groups (e.g. populations). We demonstrate its utility using sequence data from 50 Plasmodium falciparum isolates comprising two different continents and confirm known signals from genomic regions that contain important antigenic and anti-malarial drug-resistance genes.
The C++-based software VarB and user manual are available from www.pathogenseq.org/varb.
目前迫切需要工具来实时分析和可视化单核苷酸多态性、插入和缺失以及其他来自新序列文件格式的结构变体。我们开发了 VarB 软件，可用于实时可视化变异调用格式文件，并识别处于平衡选择下的区域和信息标记，以区分用户定义的组（例如人群）。我们使用来自包含两个不同大陆的 50 个恶性疟原虫分离株的序列数据证明了其效用，并确认了包含重要抗原和抗疟药物耐药基因的基因组区域中的已知信号。
基于 C++的软件 VarB 和用户手册可从 www.pathogenseq.org/varb 获取。
