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 -  Signal peptide prediction using Phobius (http://phobius.sbc.su.se/) on sequences present in phytozome_V12.tar.gz.

- phytozome_V12_signalp.tar.gz -  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 mdragicevic@ibiss.bg.ac.rs.