Additional file 13 of Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

Additional file 13 Table S8. Putative G-quadruplex-forming sequences in the genomes of Plasmodium parasites, found by G4 Hunter. Genomes were downloaded from PlasmoDB, v. 44, and searched using G4 Hunter with the parameters: threshold: 1.7, window size: 25, csv data: grouped. An additional search of the P. falciparum genome was also conducted at a lower threshold of 1.25. As per the G4 Hunter algorithm, PQSs on the reverse complement sequence had negative scores, and all locations were reported relative to the 5′ end of the sense strand. The “Strand (cf gene or nearest gene)” category was denoted as antisense if the PQS was on the opposite strand of its nearest gene, or sense if the PQS was on the same strand as its nearest gene. The “distance from nearest gene” was positive if the PQS was upstream of the nearest gene, negative if the PQS was downstream of the nearest gene, or equal to 0 if the PQS was in the coding sequence of the nearest gene.

附加文件13 表S8：疟原虫基因组中经G4 Hunter鉴定的潜在G-四链体形成序列（G-quadruplex-forming sequences）。研究所用疟原虫基因组均下载自PlasmoDB数据库v44版本，采用G4 Hunter工具进行检索，检索参数设置为：阈值1.7、窗口大小25、CSV数据分组输出。此外，针对恶性疟原虫（Plasmodium falciparum）基因组还以更低阈值1.25开展了补充检索。根据G4 Hunter算法规则，反向互补序列上的潜在G-四链体序列（PQSs, Putative G-quadruplex-forming sequences）评分为负值，所有位点均相对于有义链（sense strand）的5'端进行标注。“链类型（参照基因或邻近基因）”分类项中，若潜在G-四链体序列位于其邻近基因的互补链，则标注为反义链（antisense）；若位于与邻近基因相同的链，则标注为有义链（sense）。“与邻近基因的间距”字段中，若潜在G-四链体序列位于邻近基因上游，则间距为正值；若位于下游则为负值；若处于邻近基因的编码序列内，则间距为0。