Department of Bacteriology, National Veterinary Institute (SVA), Uppsala, Sweden.
PLoS One. 2012;7(6):e39107. doi: 10.1371/journal.pone.0039107. Epub 2012 Jun 18.
The rapid development of Next Generation Sequencing technologies leads to the accumulation of huge amounts of sequencing data. The scientific community faces an enormous challenge in how to deal with this explosion. Here we present a software tool, 'Gegenees', that uses a fragmented alignment approach to facilitate the comparative analysis of hundreds of microbial genomes. The genomes are fragmented and compared, all against all, by a multithreaded BLAST control engine. Ready-made alignments can be complemented with new genomes without recalculating the existing data points. Gegenees gives a phylogenomic overview of the genomes and the alignment can then be mined for genomic regions with conservation patterns matching a defined target group and absent from a background group. The genomic regions are given biomarker scores forming a uniqueness signature that can be viewed and explored, graphically and in tabular form. A primer/probe alignment tool is also included for specificity verification of currently used or new primers. We exemplify the use of Gegenees on the Bacillus cereus group, on Foot and Mouth Disease Viruses, and on strains from the 2011 Escherichia coli O104:H4 outbreak. Gegenees contributes towards an increased capacity of fast and efficient data mining as more and more genomes become sequenced.
下一代测序技术的快速发展导致了大量测序数据的积累。科学界面临着如何应对这一爆炸式增长的巨大挑战。在这里，我们介绍了一种名为“Gegenees”的软件工具，它使用碎片化对齐方法来促进数百个微生物基因组的比较分析。通过多线程 BLAST 控制引擎，对基因组进行碎片化处理，并对所有基因组进行两两比较。准备好的对齐可以通过添加新的基因组来补充，而无需重新计算现有数据点。Gegenees 提供了基因组的系统发育概述，然后可以对具有与定义的目标组匹配且不存在于背景组中的保守模式的基因组区域进行挖掘。基因组区域被赋予生物标志物评分，形成独特性特征，可以以图形和表格形式查看和探索。还包括一个引物/探针对齐工具，用于验证当前使用或新的引物的特异性。我们在蜡状芽孢杆菌组、口蹄疫病毒以及 2011 年大肠杆菌 O104:H4 爆发菌株上举例说明了 Gegenees 的使用。随着越来越多的基因组被测序，Gegenees 有助于提高快速高效数据挖掘的能力。
