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

<p>Hydroxyproline aware annotation of&nbsp;hydroxyproline-rich glycoprotein&nbsp;(HRGP) sequences was performed on&nbsp;sequence data from 62 plant proteomes obtained from Phytozome database (<a href="https://phytozome.jgi.doe.gov/pz/portal.html">https://phytozome.jgi.doe.gov/pz/portal.html</a>, version 12) using the&nbsp;ragp R package (<a href="https://github.com/missuse/ragp">https://github.com/missuse/ragp</a>, version 0.3.0.0001).&nbsp;</p> <p>In each archive a single comma separated value table (.csv)&nbsp;is present along with a README.txt file describing the contents of the corresponding .csv file. The archives are:</p> <p>- phytozome_V12.tar.gz - sequences from&nbsp;62 plant proteomes (phytozome V12) with a total of&nbsp;2797062 protein sequences.</p> <p>- phytozome_V12_phobius.tar.gz -<strong>&nbsp;</strong>&nbsp;Signal peptide prediction using Phobius&nbsp;(<a href="http://phobius.sbc.su.se/">http://phobius.sbc.su.se/</a>) on sequences present in&nbsp;phytozome_V12.tar.gz.</p> <p>-&nbsp;phytozome_V12_signalp.tar.gz&nbsp;-<strong>&nbsp;</strong>&nbsp;Signal peptide prediction using SignalP&nbsp;4.1 (<a href="http://www.cbs.dtu.dk/services/SignalP-4.1/">http://www.cbs.dtu.dk/services/SignalP-4.1/</a>) on sequences present in&nbsp;phytozome_V12.tar.gz.</p> <p>- phytozome_V12_targetp.tar.gz -&nbsp;Signal peptide prediction using TargetP&nbsp;1.1 (<a href="http://www.cbs.dtu.dk/services/TargetP/">http://www.cbs.dtu.dk/services/TargetP/</a>) on sequences present in&nbsp;phytozome_V12.tar.gz.</p> <p>-&nbsp;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&nbsp;&nbsp;(using Phobius,&nbsp;SignalP&nbsp;4.1 and TargetP&nbsp;1.1).</p> <p>-&nbsp;phytozome_V12_maab.tar.gz - Motif and amino acid bias (MAAB) classification of&nbsp;hydroxyproline-rich glycoproteins performed on 266135 protein sequences which were predicted to be secreted by a majority vote&nbsp;&nbsp;(using Phobius,&nbsp;SignalP&nbsp;4.1 and TargetP&nbsp;1.1). The number of predicted hydroxyprolines in each sequence is also indicated (based on predictions&nbsp;provided in phytozome_V12_predict_hyp.tar.gz).</p> <p>-&nbsp;phytozome_V12_scan_ag.tar.gz. - Hydroxyproline aware arabinogalactan motif scan&nbsp;performed on&nbsp;266135 protein sequences which were predicted to be secreted by a majority vote&nbsp;&nbsp;(using Phobius,&nbsp;SignalP&nbsp;4.1 and TargetP&nbsp;1.1). Hydroxyproline&nbsp;predictions are provided in phytozome_V12_predict_hyp.tar.gz.&nbsp;</p> <p>-&nbsp;phytozome_V12_scan_ag_hmmscan.tar.gz -&nbsp;Detection of domains&nbsp;in a subset of protein sequences which were found to contain arabinogalactan motifs (a subset of phytozome_V12_scan_ag.tar.gz).</p> <p>The list of the&nbsp;62 plant species is provided in phytozome_V12.tar.gz README.txt.</p> <p>For questions contact&nbsp;mdragicevic@ibiss.bg.ac.rs.</p> <p>&nbsp;</p> <p>&nbsp;</p>