Ioannides Andreas N, Katsani Katerina R, Ouzounis Christos A, Promponas Vasilis J
Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia 1678, Cyprus.
Department of Molecular Biology & Genetics, Democritus University of Thrace, Alexandroupolis 68100, Greece.
NAR Genom Bioinform. 2023 Mar 23;5(1):lqad025. doi: 10.1093/nargab/lqad025. eCollection 2023 Mar.
The nuclear pore complex exhibits different manifestations across eukaryotes, with certain components being restricted to specific clades. Several studies have been conducted to delineate the nuclear pore complex composition in various model organisms. Due to its pivotal role in cell viability, traditional lab experiments, such as gene knockdowns, can prove inconclusive and need to be complemented by a high-quality computational process. Here, using an extensive data collection, we create a robust library of nucleoporin protein sequences and their respective family-specific position-specific scoring matrices. By extensively validating each profile in different settings, we propose that the created profiles can be used to detect nucleoporins in proteomes with high sensitivity and specificity compared to existing methods. This library of profiles and the underlying sequence data can be used for the detection of nucleoporins in target proteomes.
核孔复合体在真核生物中表现出不同的形式，某些成分局限于特定的进化枝。已经进行了多项研究来描绘各种模式生物中的核孔复合体组成。由于其在细胞活力中的关键作用，传统的实验室实验，如基因敲低，可能无法得出结论，需要通过高质量的计算过程来补充。在这里，我们通过广泛的数据收集，创建了一个强大的核孔蛋白序列库及其各自家族特异性的位置特异性评分矩阵。通过在不同环境中广泛验证每个图谱，我们提出，与现有方法相比，创建的图谱可用于以高灵敏度和特异性检测蛋白质组中的核孔蛋白。这个图谱库和基础序列数据可用于检测目标蛋白质组中的核孔蛋白。
