Supplementary Data: A multiple genome alignment workflow shows the impact of masking and parameter tuning on alignment of functional regions in plants

This dataset includes all Supplementary Data for the preprint titled "A multiple genome alignment workflow shows the impact of masking and parameter tuning on alignment of functional regions in plants". The data predominantly consists of Excel spreadsheets describing summary statistics and metrics for alignments of plant genomes. Full descriptive names of all enclosed files are listed below. Supplementary Data S1. Repeat masking results for grass genomes using three masking methodsSupplementary Data S2. Alignment metrics for whole genome pairwise alignmentSupplementary Data S3. Alignment metrics for whole genome multiple alignmentSupplementary Data S4. List of genes in the Sorghum mini-genomeSupplementary Data S5. List of genes in the Oryza sativa mini-genomeSupplementary Data S6. Mini-genome alignment rates across speciesSupplementary Data S7. Multiple alignment summary metrics for 750 alignment parameters combinationsSupplementary Data S8. Alignment performance of high-performing parameters compared to the default parameters and the cactus alignerSupplementary Data S9. Genomic conservation scoring for multiple alignments generated with 750 alignment parameter combination compared to the default parameters Supplementary Data S10. Custom LAST penalty matrices based on substitution rates calculated from Z. mays transposon alignments

本数据集涵盖预印本论文《多重基因组比对工作流程揭示掩码策略与参数调优对植物功能区域基因组比对的影响》的全部补充数据。数据集核心为记录植物基因组比对汇总统计量与评估指标的Excel表格。下述内容列出所有附带文件的完整命名：
补充数据S1：基于三种掩码方法的禾本科基因组重复序列掩码结果
补充数据S2：全基因组两两比对评估指标
补充数据S3：全基因组多重比对评估指标
补充数据S4：高粱微型基因组基因列表
补充数据S5：水稻（Oryza sativa）微型基因组基因列表
补充数据S6：跨物种微型基因组比对率
补充数据S7：750种比对参数组合的多重比对汇总统计量
补充数据S8：高性能比对参数与默认参数及Cactus比对器的比对性能对比
补充数据S9：相较于默认参数，基于750种比对参数组合生成的多重基因组比对的基因组保守性评分
补充数据S10：基于玉米（Z. mays）转座子比对计算所得替换率构建的定制化LAST罚分矩阵