Autopolyploidy Genome Duplication Preserves Other Ancient Genome Duplications In Atlantic Salmon (Salmo Salar) Supplementary Datasets

For various species, alignments were found between a protein database (produced from Zebrafish) and the sequenced genome of that species. Using Perl scripts and the alignments, gene models were identified in the various species based on the protein sequences. The gene models, for the various species, can be found in the .gff3 files. Some of the .gff3 files have had ribosomal proteins removed. Homeologous regions were then identified using Perl scripts and can be found in .gff3 files as well. They have Homeologous_Regions.gff3 in their title. Homeologous genes in these regions were counted (named XX_XX_Homeologous_Regions.txt), and compared to all of the genes (not just homeologous genes) in these regions (named Gene_Count_Homeolgous_XX_XX_XX.txt) to find the density. Homeologous gene sequences were compared to each other to identify the Ps values between them using a program called SNAP (Files with _Homeologous_region_analysis_version_1.2.txt at the end). The analyses of these files are summarized in "Pn_Ps_Values_Vertebrate_Homeologous_Regions.ods." The synteny between species can be found in the files with .seg extensions (These can be opened in IGV). A comparison between the gene density and Ps value for each homeologous region can be found in the file, "Gene_Density_Compared_to_Ps_Values.ods." Included is an extended readme file and Perl scripts (.pl extension) in a compressed file (Final_Scripts.tar.gz).针对多个物种，研究人员在源自斑马鱼（Zebrafish）的蛋白质数据库与各物种的测序基因组之间找到了序列比对结果。研究人员借助Perl脚本与上述比对信息，基于蛋白质序列在各物种中鉴定出了基因模型（gene models）。 上述各物种的基因模型可在.gff3格式文件中获取。部分.gff3文件已剔除了核糖体蛋白相关条目。 随后，研究人员通过Perl脚本鉴定出了同源区域（homeologous regions），此类区域的相关信息同样可在.gff3格式文件中找到，其文件名包含Homeologous_Regions.gff3字样。 研究人员对这些区域内的同源基因进行了计数，对应文件命名为XX_XX_Homeologous_Regions.txt，并将该计数结果与这些区域内的全部基因（而非仅同源基因）进行对比，对应文件命名为Gene_Count_Homeolgous_XX_XX_XX.txt，以此计算基因密度。 研究人员借助名为SNAP的程序对同源基因序列进行两两比对，以计算其间的Ps值，相关文件的后缀为_Homeologous_region_analysis_version_1.2.txt。 上述文件的分析结果已汇总至"Pn_Ps_Values_Vertebrate_Homeologous_Regions.ods"文件中。 物种间的共线性（synteny）信息可在.seg格式的文件中获取，此类文件可通过IGV打开查看。 各同源区域的基因密度与Ps值的对比分析结果可在文件"Gene_Density_Compared_to_Ps_Values.ods"中获取。 压缩包Final_Scripts.tar.gz中包含了扩展版说明文档与后缀为.pl的Perl脚本文件。