Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology-based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R’s rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.

中文翻译：

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ragp：在R中实施的用于开采富含植物羟脯氨酸的糖蛋白的管道

富含羟脯氨酸的糖蛋白（HRGP）是植物中发现的最复杂的大分子家族之一，这是由于装饰蛋白主链的聚糖多样性以及蛋白主链的异质性所致。尽管这种多样性负责与HRGP相关的多种生理功能，但它阻碍了基于同源性的鉴定。基于鉴定具有特征性基序和偏向氨基酸组成的序列的当前方法限于原型序列。Ragp是用于HRGP挖掘和分析的R包，重点是阿拉伯半乳聚糖蛋白。ragp过滤管道利用了HRGP的关键特征之一，即代表糖基化位点的羟脯氨酸的存在。主要包装特征包括脯氨酸羟化位点的预测，氨基酸基序和偏倚分析，与Web服务器进行有效通信以预测N末端信号肽，糖基磷脂酰肌醇修饰位点和无序区域，并基于预测的Pfam结构域通过hmmscan和随后的GO富集注释序列的能力。这样，ragp扩展了R的丰富生态系统，可用于高通量序列数据分析。ragp R软件包可在MIT开放源代码许可下获得，可从GitHub免费下载：https://github.com/missuse/ragp。ragp扩展了R的丰富生态系统，可进行高通量序列数据分析。ragp R软件包可在MIT开放源代码许可下获得，可从GitHub免费下载：https://github.com/missuse/ragp。ragp扩展了R的丰富生态系统，可进行高通量序列数据分析。ragp R软件包可在MIT开放源代码许可下获得，可从GitHub免费下载，网址为：https：//github.com/missuse/ragp。