Jean Geraldine, Nikolski Macha
Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, Germany.
Int J Bioinform Res Appl. 2011;7(1):43-62. doi: 10.1504/IJBRA.2011.039169.
Current methods for detecting synteny work well for genomes with high degrees of inter- and intra-species chromosomal homology, such as mammals. This paper presents a new algorithm for synteny computation that is well suited to genomes covering a large evolutionary span. It is based on a three-step process: identification of initial microsyntenic homologous regions, extension of homologous boundaries and reconstruction of syntenic blocks by identification of groups of homologous genomic segments that are conserved in every subject genome. Our method performs as well as GRIMM-Synteny on mammalian genomes, and outperforms it for clades with much greater evolutionary distances such as the Hemiascomycetous yeasts.
目前用于检测共线性的方法对于具有高度种间和种内染色体同源性的基因组（如哺乳动物基因组）效果良好。本文提出了一种新的共线性计算算法，该算法非常适合覆盖较大进化跨度的基因组。它基于一个三步过程：识别初始微共线性同源区域、扩展同源边界以及通过识别在每个目标基因组中保守的同源基因组片段组来重建共线性块。我们的方法在哺乳动物基因组上的表现与GRIMM-Synteny相当，而在进化距离大得多的进化枝（如半子囊菌酵母）上则优于GRIMM-Synteny。
