Annotation of Phytozome V12 protein plant sequences using the ragp pipeline for hydroxyproline-rich glycoprotein mining

Hydroxyproline aware annotation of hydroxyproline-rich glycoprotein (HRGP) sequences was performed on sequence data from 62 plant proteomes obtained from Phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html, version 12) using the ragp R package (https://github.com/missuse/ragp, version 0.3.0.0001). In each archive a single comma separated value table (.csv) is present along with a README.txt file describing the contents of the corresponding .csv file. The archives are: - phytozome_V12.tar.gz - sequences from 62 plant proteomes (phytozome V12) with a total of 2797062 protein sequences. - phytozome_V12_phobius.tar.gz -<strong> </strong> Signal peptide prediction using Phobius (http://phobius.sbc.su.se/) on sequences present in phytozome_V12.tar.gz. - phytozome_V12_signalp.tar.gz -<strong> </strong> Signal peptide prediction using SignalP 4.1 (http://www.cbs.dtu.dk/services/SignalP-4.1/) on sequences present in phytozome_V12.tar.gz. - phytozome_V12_targetp.tar.gz - Signal peptide prediction using TargetP 1.1 (http://www.cbs.dtu.dk/services/TargetP/) on sequences present in phytozome_V12.tar.gz. - phytozome_V12_predict_hyp.tar.gz - Probability of proline hydroxylation for each proline from 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1). - phytozome_V12_maab.tar.gz - Motif and amino acid bias (MAAB) classification of hydroxyproline-rich glycoproteins performed on 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1). The number of predicted hydroxyprolines in each sequence is also indicated (based on predictions provided in phytozome_V12_predict_hyp.tar.gz). - phytozome_V12_scan_ag.tar.gz. - Hydroxyproline aware arabinogalactan motif scan performed on 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1). Hydroxyproline predictions are provided in phytozome_V12_predict_hyp.tar.gz. - phytozome_V12_scan_ag_hmmscan.tar.gz - Detection of domains in a subset of protein sequences which were found to contain arabinogalactan motifs (a subset of phytozome_V12_scan_ag.tar.gz). The list of the 62 plant species is provided in phytozome_V12.tar.gz README.txt. For questions contact [e-mail].针对富含羟脯氨酸的糖蛋白（hydroxyproline-rich glycoprotein, HRGP）序列的羟脯氨酸感知型注释，基于从Phytozome数据库（https://phytozome.jgi.doe.gov/pz/portal.html，版本12）获取的62个植物蛋白质组序列数据，借助ragp R包（https://github.com/missuse/ragp，版本0.3.0.0001）完成。 每个归档包内均包含一份逗号分隔值表格（.csv）与一份README.txt文件，用于说明对应csv文件的内容。各归档包详情如下： - phytozome_V12.tar.gz：涵盖62个植物蛋白质组的序列（对应phytozome V12版本），总计包含2797062条蛋白质序列。 - phytozome_V12_phobius.tar.gz：针对phytozome_V12.tar.gz中的序列，使用Phobius（http://phobius.sbc.su.se/）完成信号肽预测的结果文件。 - phytozome_V12_signalp.tar.gz：针对phytozome_V12.tar.gz中的序列，使用SignalP 4.1（http://www.cbs.dtu.dk/services/SignalP-4.1/）完成信号肽预测的结果文件。 - phytozome_V12_targetp.tar.gz：针对phytozome_V12.tar.gz中的序列，使用TargetP 1.1（http://www.cbs.dtu.dk/services/TargetP/）完成信号肽预测的结果文件。 - phytozome_V12_predict_hyp.tar.gz：针对通过Phobius、SignalP 4.1与TargetP 1.1工具多数投票预测为分泌型的266135条蛋白质序列，计算每条序列中每个脯氨酸的羟脯氨酸化概率。 - phytozome_V12_maab.tar.gz：针对通过Phobius、SignalP 4.1与TargetP 1.1工具多数投票预测为分泌型的266135条蛋白质序列，开展富含羟脯氨酸的糖蛋白的基序与氨基酸偏好性（Motif and amino acid bias, MAAB）分类，同时标注每条序列中预测得到的羟脯氨酸数量（该数据基于phytozome_V12_predict_hyp.tar.gz中的预测结果）。 - phytozome_V12_scan_ag.tar.gz：针对通过Phobius、SignalP 4.1与TargetP 1.1工具多数投票预测为分泌型的266135条蛋白质序列，开展基于羟脯氨酸感知的阿拉伯半乳聚糖基序扫描，羟脯氨酸预测结果取自phytozome_V12_predict_hyp.tar.gz。 - phytozome_V12_scan_ag_hmmscan.tar.gz：针对phytozome_V12_scan_ag.tar.gz中被检出含有阿拉伯半乳聚糖基序的蛋白质序列子集，完成结构域识别分析。 62种植物的物种列表可在phytozome_V12.tar.gz的README.txt文件中查阅。如有相关疑问，请联系邮箱[e-mail]。