Julian Alexander Thomas, Pombert Jean-François
Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA.
bioRxiv. 2024 May 13:2024.05.09.593317. doi: 10.1101/2024.05.09.593317.
Investigating collinearity between chromosomes is often used in comparative genomics to help identify gene orthologs, pinpoint genes that might have been overlooked as part of annotation processes and/or perform various evolutionary inferences. Collinear segments, also known as syntenic blocks, can be inferred from sequence alignments and/or from the identification of genes arrayed in the same order and relative orientations between investigated genomes. To help perform these analyses and assess their outcomes, we built a simple pipeline called SYNY (for synteny) that implements the two distinct approaches and produces different visualizations. The SYNY pipeline was built with ease of use in mind and runs on modest hardware. The pipeline is written in Perl and Python and is available on GitHub (https://github.com/PombertLab/SYNY) under the permissive MIT license.
在比较基因组学中，研究染色体之间的共线性常用于帮助识别基因直系同源物、找出在注释过程中可能被忽视的基因和/或进行各种进化推断。共线片段，也称为同线区块，可以从序列比对和/或从所研究基因组之间以相同顺序和相对方向排列的基因识别中推断出来。为了帮助进行这些分析并评估其结果，我们构建了一个名为SYNY（用于同线性）的简单流程，该流程实现了两种不同的方法并生成不同的可视化结果。SYNY流程在设计时考虑了易用性，可在普通硬件上运行。该流程用Perl和Python编写，根据宽松的MIT许可协议在GitHub（https://github.com/PombertLab/SYNY）上可用。
